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Commit 54a3c39a by Mustafa Tekpinar
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Moved extractQuerySeq from gemmeAnal.py to sgemme.py.

parent faafebd8
Showing with 27 additions and 954 deletions
gemmeAnal.py
...@@ -133,7 +133,9 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -133,7 +133,9 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
chainID = chains[0] chainID = chains[0]
#TODO: Remove Bash dependency here. Make the copying process in Python
subprocess.call("cp $SGEMME_PATH/default.conf .",shell=True) subprocess.call("cp $SGEMME_PATH/default.conf .",shell=True)
if retMet=="input": if retMet=="input":
if bFile!='': if bFile!='':
#TODO: I think these two lines must be here as well but I am not sure. #TODO: I think these two lines must be here as well but I am not sure.
......
sgemme.py
...@@ -22,6 +22,30 @@ from gemmeAnal import * ...@@ -22,6 +22,30 @@ from gemmeAnal import *
import pandas as pd import pandas as pd
def extractQuerySeq(filename):
"""
# Extract the query sequence from the input alignment
"""
fIN = open(filename,"r")
lines = fIN.readlines()
fIN.close()
if lines[0][0]!=">":
raise Exception('bad FASTA format')
else:
prot = re.compile("[^A-Z0-9a-z]").split(lines[0][1:])[0]
fOUT = open(prot+".fasta","w")
fOUT.write(">"+prot+"\n")
seq=""
i = 1
while lines[i][0]!=">":
seq = seq + lines[i].strip().strip(".").strip("-")
fOUT.write(lines[i])
i = i + 1
fOUT.close()
return prot,seq,i-1
def rankSortProteinData(dataArray, inverted=True): def rankSortProteinData(dataArray, inverted=True):
""" """
This function ranksorts protein data and converts it This function ranksorts protein data and converts it
......
tests/BLAT.fasta deleted 100644 → 0
>BLAT
HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVL
LCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSA
AITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPN
DERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSAL
PAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNR
QIAEIGASLIKHW
tests/BLAT.out deleted 100644 → 0
***** Format Files ******
copy file:/home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT.pdb
***** End Format Files ******
***** JET analysis ******
Alignment file:/home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_A.fasta
Analysis of sequence: A
/home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_A.fasta
format ok
Selected 14782 sequences before filtering
Filtering sequences (Iteration 1):
-Identity: Removed 0 seqs
-Redundancy: Removed 1446 seqs
-Similar names: Removed 0 seqs
-Gaps: Removed 0 seqs
-Length: Removed 0 seqs
-EValue: Removed 0 seqs
-CPU Load: Removed 0 seqs
Selected 13336 after filtering
Filtering sequences (Iteration 2):
-Identity: Removed 2834 seqs
-Redundancy: Removed 0 seqs
-Similar names: Removed 0 seqs
-Gaps: Removed 0 seqs
-Length: Removed 0 seqs
-EValue: Removed 0 seqs
-CPU Load: Removed 8604 seqs
Selected 1898 after filtering
Nb alignments:43 Nb sequences:43
Final iterated blast partition:498 498 456 446
proportion=0.5
selected partition: 11 11 11 10
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_0.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_0.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_1.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_1.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_2.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_2.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_3.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_3.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_4.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_4.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_5.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_5.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_6.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_6.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_7.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_7.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_8.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_8.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_9.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_9.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_10.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_10.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_11.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_11.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_12.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_12.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_13.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_13.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_14.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_14.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_15.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_15.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_16.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_16.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_17.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_17.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_18.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_18.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_19.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_19.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_20.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_20.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_21.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_21.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_22.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_22.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_23.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_23.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_24.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_24.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_25.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_25.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_26.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_26.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_27.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_27.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_28.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_28.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_29.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_29.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_30.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_30.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_31.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_31.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_32.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_32.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_33.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_33.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_34.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_34.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_35.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_35.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_36.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_36.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_37.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_37.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_38.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_38.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_39.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_39.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_40.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_40.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_41.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_41.aln
Exit value: 0
**********write**********
Command: /usr/bin/muscle -in /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_42.fasta -clw -out /home/tekpinar/research/carbone-lab-software/GEMME/example/BLAT/BLAT_42.aln
Exit value: 0
***** End JET analysis ******
tests/BLAT.pdb deleted 100644 → 0
ATOM 1 CA HIS A 1 43.524 70.381 46.465 1.00 0.0
ATOM 2 CA PRO A 2 43.524 70.381 46.465 1.00 0.0
ATOM 3 CA GLU A 3 43.524 70.381 46.465 1.00 0.0
ATOM 4 CA THR A 4 43.524 70.381 46.465 1.00 0.0
ATOM 5 CA LEU A 5 43.524 70.381 46.465 1.00 0.0
ATOM 6 CA VAL A 6 43.524 70.381 46.465 1.00 0.0
ATOM 7 CA LYS A 7 43.524 70.381 46.465 1.00 0.0
ATOM 8 CA VAL A 8 43.524 70.381 46.465 1.00 0.0
ATOM 9 CA LYS A 9 43.524 70.381 46.465 1.00 0.0
ATOM 10 CA ASP A 10 43.524 70.381 46.465 1.00 0.0
ATOM 11 CA ALA A 11 43.524 70.381 46.465 1.00 0.0
ATOM 12 CA GLU A 12 43.524 70.381 46.465 1.00 0.0
ATOM 13 CA ASP A 13 43.524 70.381 46.465 1.00 0.0
ATOM 14 CA GLN A 14 43.524 70.381 46.465 1.00 0.0
ATOM 15 CA LEU A 15 43.524 70.381 46.465 1.00 0.0
ATOM 16 CA GLY A 16 43.524 70.381 46.465 1.00 0.0
ATOM 17 CA ALA A 17 43.524 70.381 46.465 1.00 0.0
ATOM 18 CA ARG A 18 43.524 70.381 46.465 1.00 0.0
ATOM 19 CA VAL A 19 43.524 70.381 46.465 1.00 0.0
ATOM 20 CA GLY A 20 43.524 70.381 46.465 1.00 0.0
ATOM 21 CA TYR A 21 43.524 70.381 46.465 1.00 0.0
ATOM 22 CA ILE A 22 43.524 70.381 46.465 1.00 0.0
ATOM 23 CA GLU A 23 43.524 70.381 46.465 1.00 0.0
ATOM 24 CA LEU A 24 43.524 70.381 46.465 1.00 0.0
ATOM 25 CA ASP A 25 43.524 70.381 46.465 1.00 0.0
ATOM 26 CA LEU A 26 43.524 70.381 46.465 1.00 0.0
ATOM 27 CA ASN A 27 43.524 70.381 46.465 1.00 0.0
ATOM 28 CA SER A 28 43.524 70.381 46.465 1.00 0.0
ATOM 29 CA GLY A 29 43.524 70.381 46.465 1.00 0.0
ATOM 30 CA LYS A 30 43.524 70.381 46.465 1.00 0.0
ATOM 31 CA ILE A 31 43.524 70.381 46.465 1.00 0.0
ATOM 32 CA LEU A 32 43.524 70.381 46.465 1.00 0.0
ATOM 33 CA GLU A 33 43.524 70.381 46.465 1.00 0.0
ATOM 34 CA SER A 34 43.524 70.381 46.465 1.00 0.0
ATOM 35 CA PHE A 35 43.524 70.381 46.465 1.00 0.0
ATOM 36 CA ARG A 36 43.524 70.381 46.465 1.00 0.0
ATOM 37 CA PRO A 37 43.524 70.381 46.465 1.00 0.0
ATOM 38 CA GLU A 38 43.524 70.381 46.465 1.00 0.0
ATOM 39 CA GLU A 39 43.524 70.381 46.465 1.00 0.0
ATOM 40 CA ARG A 40 43.524 70.381 46.465 1.00 0.0
ATOM 41 CA PHE A 41 43.524 70.381 46.465 1.00 0.0
ATOM 42 CA PRO A 42 43.524 70.381 46.465 1.00 0.0
ATOM 43 CA MET A 43 43.524 70.381 46.465 1.00 0.0
ATOM 44 CA MET A 44 43.524 70.381 46.465 1.00 0.0
ATOM 45 CA SER A 45 43.524 70.381 46.465 1.00 0.0
ATOM 46 CA THR A 46 43.524 70.381 46.465 1.00 0.0
ATOM 47 CA PHE A 47 43.524 70.381 46.465 1.00 0.0
ATOM 48 CA LYS A 48 43.524 70.381 46.465 1.00 0.0
ATOM 49 CA VAL A 49 43.524 70.381 46.465 1.00 0.0
ATOM 50 CA LEU A 50 43.524 70.381 46.465 1.00 0.0
ATOM 51 CA LEU A 51 43.524 70.381 46.465 1.00 0.0
ATOM 52 CA CYS A 52 43.524 70.381 46.465 1.00 0.0
ATOM 53 CA GLY A 53 43.524 70.381 46.465 1.00 0.0
ATOM 54 CA ALA A 54 43.524 70.381 46.465 1.00 0.0
ATOM 55 CA VAL A 55 43.524 70.381 46.465 1.00 0.0
ATOM 56 CA LEU A 56 43.524 70.381 46.465 1.00 0.0
ATOM 57 CA SER A 57 43.524 70.381 46.465 1.00 0.0
ATOM 58 CA ARG A 58 43.524 70.381 46.465 1.00 0.0
ATOM 59 CA VAL A 59 43.524 70.381 46.465 1.00 0.0
ATOM 60 CA ASP A 60 43.524 70.381 46.465 1.00 0.0
ATOM 61 CA ALA A 61 43.524 70.381 46.465 1.00 0.0
ATOM 62 CA GLY A 62 43.524 70.381 46.465 1.00 0.0
ATOM 63 CA GLN A 63 43.524 70.381 46.465 1.00 0.0
ATOM 64 CA GLU A 64 43.524 70.381 46.465 1.00 0.0
ATOM 65 CA GLN A 65 43.524 70.381 46.465 1.00 0.0
ATOM 66 CA LEU A 66 43.524 70.381 46.465 1.00 0.0
ATOM 67 CA GLY A 67 43.524 70.381 46.465 1.00 0.0
ATOM 68 CA ARG A 68 43.524 70.381 46.465 1.00 0.0
ATOM 69 CA ARG A 69 43.524 70.381 46.465 1.00 0.0
ATOM 70 CA ILE A 70 43.524 70.381 46.465 1.00 0.0
ATOM 71 CA HIS A 71 43.524 70.381 46.465 1.00 0.0
ATOM 72 CA TYR A 72 43.524 70.381 46.465 1.00 0.0
ATOM 73 CA SER A 73 43.524 70.381 46.465 1.00 0.0
ATOM 74 CA GLN A 74 43.524 70.381 46.465 1.00 0.0
ATOM 75 CA ASN A 75 43.524 70.381 46.465 1.00 0.0
ATOM 76 CA ASP A 76 43.524 70.381 46.465 1.00 0.0
ATOM 77 CA LEU A 77 43.524 70.381 46.465 1.00 0.0
ATOM 78 CA VAL A 78 43.524 70.381 46.465 1.00 0.0
ATOM 79 CA GLU A 79 43.524 70.381 46.465 1.00 0.0
ATOM 80 CA TYR A 80 43.524 70.381 46.465 1.00 0.0
ATOM 81 CA SER A 81 43.524 70.381 46.465 1.00 0.0
ATOM 82 CA PRO A 82 43.524 70.381 46.465 1.00 0.0
ATOM 83 CA VAL A 83 43.524 70.381 46.465 1.00 0.0
ATOM 84 CA THR A 84 43.524 70.381 46.465 1.00 0.0
ATOM 85 CA GLU A 85 43.524 70.381 46.465 1.00 0.0
ATOM 86 CA LYS A 86 43.524 70.381 46.465 1.00 0.0
ATOM 87 CA HIS A 87 43.524 70.381 46.465 1.00 0.0
ATOM 88 CA LEU A 88 43.524 70.381 46.465 1.00 0.0
ATOM 89 CA THR A 89 43.524 70.381 46.465 1.00 0.0
ATOM 90 CA ASP A 90 43.524 70.381 46.465 1.00 0.0
ATOM 91 CA GLY A 91 43.524 70.381 46.465 1.00 0.0
ATOM 92 CA MET A 92 43.524 70.381 46.465 1.00 0.0
ATOM 93 CA THR A 93 43.524 70.381 46.465 1.00 0.0
ATOM 94 CA VAL A 94 43.524 70.381 46.465 1.00 0.0
ATOM 95 CA ARG A 95 43.524 70.381 46.465 1.00 0.0
ATOM 96 CA GLU A 96 43.524 70.381 46.465 1.00 0.0
ATOM 97 CA LEU A 97 43.524 70.381 46.465 1.00 0.0
ATOM 98 CA CYS A 98 43.524 70.381 46.465 1.00 0.0
ATOM 99 CA SER A 99 43.524 70.381 46.465 1.00 0.0
ATOM 100 CA ALA A 100 43.524 70.381 46.465 1.00 0.0
ATOM 101 CA ALA A 101 43.524 70.381 46.465 1.00 0.0
ATOM 102 CA ILE A 102 43.524 70.381 46.465 1.00 0.0
ATOM 103 CA THR A 103 43.524 70.381 46.465 1.00 0.0
ATOM 104 CA MET A 104 43.524 70.381 46.465 1.00 0.0
ATOM 105 CA SER A 105 43.524 70.381 46.465 1.00 0.0
ATOM 106 CA ASP A 106 43.524 70.381 46.465 1.00 0.0
ATOM 107 CA ASN A 107 43.524 70.381 46.465 1.00 0.0
ATOM 108 CA THR A 108 43.524 70.381 46.465 1.00 0.0
ATOM 109 CA ALA A 109 43.524 70.381 46.465 1.00 0.0
ATOM 110 CA ALA A 110 43.524 70.381 46.465 1.00 0.0
ATOM 111 CA ASN A 111 43.524 70.381 46.465 1.00 0.0
ATOM 112 CA LEU A 112 43.524 70.381 46.465 1.00 0.0
ATOM 113 CA LEU A 113 43.524 70.381 46.465 1.00 0.0
ATOM 114 CA LEU A 114 43.524 70.381 46.465 1.00 0.0
ATOM 115 CA THR A 115 43.524 70.381 46.465 1.00 0.0
ATOM 116 CA THR A 116 43.524 70.381 46.465 1.00 0.0
ATOM 117 CA ILE A 117 43.524 70.381 46.465 1.00 0.0
ATOM 118 CA GLY A 118 43.524 70.381 46.465 1.00 0.0
ATOM 119 CA GLY A 119 43.524 70.381 46.465 1.00 0.0
ATOM 120 CA PRO A 120 43.524 70.381 46.465 1.00 0.0
ATOM 121 CA LYS A 121 43.524 70.381 46.465 1.00 0.0
ATOM 122 CA GLU A 122 43.524 70.381 46.465 1.00 0.0
ATOM 123 CA LEU A 123 43.524 70.381 46.465 1.00 0.0
ATOM 124 CA THR A 124 43.524 70.381 46.465 1.00 0.0
ATOM 125 CA ALA A 125 43.524 70.381 46.465 1.00 0.0
ATOM 126 CA PHE A 126 43.524 70.381 46.465 1.00 0.0
ATOM 127 CA LEU A 127 43.524 70.381 46.465 1.00 0.0
ATOM 128 CA HIS A 128 43.524 70.381 46.465 1.00 0.0
ATOM 129 CA ASN A 129 43.524 70.381 46.465 1.00 0.0
ATOM 130 CA MET A 130 43.524 70.381 46.465 1.00 0.0
ATOM 131 CA GLY A 131 43.524 70.381 46.465 1.00 0.0
ATOM 132 CA ASP A 132 43.524 70.381 46.465 1.00 0.0
ATOM 133 CA HIS A 133 43.524 70.381 46.465 1.00 0.0
ATOM 134 CA VAL A 134 43.524 70.381 46.465 1.00 0.0
ATOM 135 CA THR A 135 43.524 70.381 46.465 1.00 0.0
ATOM 136 CA ARG A 136 43.524 70.381 46.465 1.00 0.0
ATOM 137 CA LEU A 137 43.524 70.381 46.465 1.00 0.0
ATOM 138 CA ASP A 138 43.524 70.381 46.465 1.00 0.0
ATOM 139 CA ARG A 139 43.524 70.381 46.465 1.00 0.0
ATOM 140 CA TRP A 140 43.524 70.381 46.465 1.00 0.0
ATOM 141 CA GLU A 141 43.524 70.381 46.465 1.00 0.0
ATOM 142 CA PRO A 142 43.524 70.381 46.465 1.00 0.0
ATOM 143 CA GLU A 143 43.524 70.381 46.465 1.00 0.0
ATOM 144 CA LEU A 144 43.524 70.381 46.465 1.00 0.0
ATOM 145 CA ASN A 145 43.524 70.381 46.465 1.00 0.0
ATOM 146 CA GLU A 146 43.524 70.381 46.465 1.00 0.0
ATOM 147 CA ALA A 147 43.524 70.381 46.465 1.00 0.0
ATOM 148 CA ILE A 148 43.524 70.381 46.465 1.00 0.0
ATOM 149 CA PRO A 149 43.524 70.381 46.465 1.00 0.0
ATOM 150 CA ASN A 150 43.524 70.381 46.465 1.00 0.0
ATOM 151 CA ASP A 151 43.524 70.381 46.465 1.00 0.0
ATOM 152 CA GLU A 152 43.524 70.381 46.465 1.00 0.0
ATOM 153 CA ARG A 153 43.524 70.381 46.465 1.00 0.0
ATOM 154 CA ASP A 154 43.524 70.381 46.465 1.00 0.0
ATOM 155 CA THR A 155 43.524 70.381 46.465 1.00 0.0
ATOM 156 CA THR A 156 43.524 70.381 46.465 1.00 0.0
ATOM 157 CA MET A 157 43.524 70.381 46.465 1.00 0.0
ATOM 158 CA PRO A 158 43.524 70.381 46.465 1.00 0.0
ATOM 159 CA ALA A 159 43.524 70.381 46.465 1.00 0.0
ATOM 160 CA ALA A 160 43.524 70.381 46.465 1.00 0.0
ATOM 161 CA MET A 161 43.524 70.381 46.465 1.00 0.0
ATOM 162 CA ALA A 162 43.524 70.381 46.465 1.00 0.0
ATOM 163 CA THR A 163 43.524 70.381 46.465 1.00 0.0
ATOM 164 CA THR A 164 43.524 70.381 46.465 1.00 0.0
ATOM 165 CA LEU A 165 43.524 70.381 46.465 1.00 0.0
ATOM 166 CA ARG A 166 43.524 70.381 46.465 1.00 0.0
ATOM 167 CA LYS A 167 43.524 70.381 46.465 1.00 0.0
ATOM 168 CA LEU A 168 43.524 70.381 46.465 1.00 0.0
ATOM 169 CA LEU A 169 43.524 70.381 46.465 1.00 0.0
ATOM 170 CA THR A 170 43.524 70.381 46.465 1.00 0.0
ATOM 171 CA GLY A 171 43.524 70.381 46.465 1.00 0.0
ATOM 172 CA GLU A 172 43.524 70.381 46.465 1.00 0.0
ATOM 173 CA LEU A 173 43.524 70.381 46.465 1.00 0.0
ATOM 174 CA LEU A 174 43.524 70.381 46.465 1.00 0.0
ATOM 175 CA THR A 175 43.524 70.381 46.465 1.00 0.0
ATOM 176 CA LEU A 176 43.524 70.381 46.465 1.00 0.0
ATOM 177 CA ALA A 177 43.524 70.381 46.465 1.00 0.0
ATOM 178 CA SER A 178 43.524 70.381 46.465 1.00 0.0
ATOM 179 CA ARG A 179 43.524 70.381 46.465 1.00 0.0
ATOM 180 CA GLN A 180 43.524 70.381 46.465 1.00 0.0
ATOM 181 CA GLN A 181 43.524 70.381 46.465 1.00 0.0
ATOM 182 CA LEU A 182 43.524 70.381 46.465 1.00 0.0
ATOM 183 CA ILE A 183 43.524 70.381 46.465 1.00 0.0
ATOM 184 CA ASP A 184 43.524 70.381 46.465 1.00 0.0
ATOM 185 CA TRP A 185 43.524 70.381 46.465 1.00 0.0
ATOM 186 CA MET A 186 43.524 70.381 46.465 1.00 0.0
ATOM 187 CA GLU A 187 43.524 70.381 46.465 1.00 0.0
ATOM 188 CA ALA A 188 43.524 70.381 46.465 1.00 0.0
ATOM 189 CA ASP A 189 43.524 70.381 46.465 1.00 0.0
ATOM 190 CA LYS A 190 43.524 70.381 46.465 1.00 0.0
ATOM 191 CA VAL A 191 43.524 70.381 46.465 1.00 0.0
ATOM 192 CA ALA A 192 43.524 70.381 46.465 1.00 0.0
ATOM 193 CA GLY A 193 43.524 70.381 46.465 1.00 0.0
ATOM 194 CA PRO A 194 43.524 70.381 46.465 1.00 0.0
ATOM 195 CA LEU A 195 43.524 70.381 46.465 1.00 0.0
ATOM 196 CA LEU A 196 43.524 70.381 46.465 1.00 0.0
ATOM 197 CA ARG A 197 43.524 70.381 46.465 1.00 0.0
ATOM 198 CA SER A 198 43.524 70.381 46.465 1.00 0.0
ATOM 199 CA ALA A 199 43.524 70.381 46.465 1.00 0.0
ATOM 200 CA LEU A 200 43.524 70.381 46.465 1.00 0.0
ATOM 201 CA PRO A 201 43.524 70.381 46.465 1.00 0.0
ATOM 202 CA ALA A 202 43.524 70.381 46.465 1.00 0.0
ATOM 203 CA GLY A 203 43.524 70.381 46.465 1.00 0.0
ATOM 204 CA TRP A 204 43.524 70.381 46.465 1.00 0.0
ATOM 205 CA PHE A 205 43.524 70.381 46.465 1.00 0.0
ATOM 206 CA ILE A 206 43.524 70.381 46.465 1.00 0.0
ATOM 207 CA ALA A 207 43.524 70.381 46.465 1.00 0.0
ATOM 208 CA ASP A 208 43.524 70.381 46.465 1.00 0.0
ATOM 209 CA LYS A 209 43.524 70.381 46.465 1.00 0.0
ATOM 210 CA SER A 210 43.524 70.381 46.465 1.00 0.0
ATOM 211 CA GLY A 211 43.524 70.381 46.465 1.00 0.0
ATOM 212 CA ALA A 212 43.524 70.381 46.465 1.00 0.0
ATOM 213 CA GLY A 213 43.524 70.381 46.465 1.00 0.0
ATOM 214 CA GLU A 214 43.524 70.381 46.465 1.00 0.0
ATOM 215 CA ARG A 215 43.524 70.381 46.465 1.00 0.0
ATOM 216 CA GLY A 216 43.524 70.381 46.465 1.00 0.0
ATOM 217 CA SER A 217 43.524 70.381 46.465 1.00 0.0
ATOM 218 CA ARG A 218 43.524 70.381 46.465 1.00 0.0
ATOM 219 CA GLY A 219 43.524 70.381 46.465 1.00 0.0
ATOM 220 CA ILE A 220 43.524 70.381 46.465 1.00 0.0
ATOM 221 CA ILE A 221 43.524 70.381 46.465 1.00 0.0
ATOM 222 CA ALA A 222 43.524 70.381 46.465 1.00 0.0
ATOM 223 CA ALA A 223 43.524 70.381 46.465 1.00 0.0
ATOM 224 CA LEU A 224 43.524 70.381 46.465 1.00 0.0
ATOM 225 CA GLY A 225 43.524 70.381 46.465 1.00 0.0
ATOM 226 CA PRO A 226 43.524 70.381 46.465 1.00 0.0
ATOM 227 CA ASP A 227 43.524 70.381 46.465 1.00 0.0
ATOM 228 CA GLY A 228 43.524 70.381 46.465 1.00 0.0
ATOM 229 CA LYS A 229 43.524 70.381 46.465 1.00 0.0
ATOM 230 CA PRO A 230 43.524 70.381 46.465 1.00 0.0
ATOM 231 CA SER A 231 43.524 70.381 46.465 1.00 0.0
ATOM 232 CA ARG A 232 43.524 70.381 46.465 1.00 0.0
ATOM 233 CA ILE A 233 43.524 70.381 46.465 1.00 0.0
ATOM 234 CA VAL A 234 43.524 70.381 46.465 1.00 0.0
ATOM 235 CA VAL A 235 43.524 70.381 46.465 1.00 0.0
ATOM 236 CA ILE A 236 43.524 70.381 46.465 1.00 0.0
ATOM 237 CA TYR A 237 43.524 70.381 46.465 1.00 0.0
ATOM 238 CA THR A 238 43.524 70.381 46.465 1.00 0.0
ATOM 239 CA THR A 239 43.524 70.381 46.465 1.00 0.0
ATOM 240 CA GLY A 240 43.524 70.381 46.465 1.00 0.0
ATOM 241 CA SER A 241 43.524 70.381 46.465 1.00 0.0
ATOM 242 CA GLN A 242 43.524 70.381 46.465 1.00 0.0
ATOM 243 CA ALA A 243 43.524 70.381 46.465 1.00 0.0
ATOM 244 CA THR A 244 43.524 70.381 46.465 1.00 0.0
ATOM 245 CA MET A 245 43.524 70.381 46.465 1.00 0.0
ATOM 246 CA ASP A 246 43.524 70.381 46.465 1.00 0.0
ATOM 247 CA GLU A 247 43.524 70.381 46.465 1.00 0.0
ATOM 248 CA ARG A 248 43.524 70.381 46.465 1.00 0.0
ATOM 249 CA ASN A 249 43.524 70.381 46.465 1.00 0.0
ATOM 250 CA ARG A 250 43.524 70.381 46.465 1.00 0.0
ATOM 251 CA GLN A 251 43.524 70.381 46.465 1.00 0.0
ATOM 252 CA ILE A 252 43.524 70.381 46.465 1.00 0.0
ATOM 253 CA ALA A 253 43.524 70.381 46.465 1.00 0.0
ATOM 254 CA GLU A 254 43.524 70.381 46.465 1.00 0.0
ATOM 255 CA ILE A 255 43.524 70.381 46.465 1.00 0.0
ATOM 256 CA GLY A 256 43.524 70.381 46.465 1.00 0.0
ATOM 257 CA ALA A 257 43.524 70.381 46.465 1.00 0.0
ATOM 258 CA SER A 258 43.524 70.381 46.465 1.00 0.0
ATOM 259 CA LEU A 259 43.524 70.381 46.465 1.00 0.0
ATOM 260 CA ILE A 260 43.524 70.381 46.465 1.00 0.0
ATOM 261 CA LYS A 261 43.524 70.381 46.465 1.00 0.0
ATOM 262 CA HIS A 262 43.524 70.381 46.465 1.00 0.0
ATOM 263 CA TRP A 263 43.524 70.381 46.465 1.00 0.0
tests/BLAT_conservation.txt deleted 100644 → 0
"1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35" "36" "37" "38" "39" "40" "41" "42" "43" "44" "45" "46" "47" "48" "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60" "61" "62" "63" "64" "65" "66" "67" "68" "69" "70" "71" "72" "73" "74" "75" "76" "77" "78" "79" "80" "81" "82" "83" "84" "85" "86" "87" "88" "89" "90" "91" "92" "93" "94" "95" "96" "97" "98" "99" "100" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" "111" "112" "113" "114" "115" "116" "117" "118" "119" "120" "121" "122" "123" "124" "125" "126" "127" "128" "129" "130" "131" "132" "133" "134" "135" "136" "137" "138" "139" "140" "141" "142" "143" "144" "145" "146" "147" "148" "149" "150" "151" "152" "153" "154" "155" "156" "157" "158" "159" "160" "161" "162" "163" "164" "165" "166" "167" "168" "169" "170" "171" "172" "173" "174" "175" "176" "177" "178" "179" "180" "181" "182" "183" "184" "185" "186" "187" "188" "189" "190" "191" "192" "193" "194" "195" "196" "197" "198" "199" "200" "201" "202" "203" "204" "205" "206" "207" "208" "209" "210" "211" "212" "213" "214" "215" "216" "217" "218" "219" "220" "221" "222" "223" "224" "225" "226" "227" "228" "229" "230" "231" "232" "233" "234" "235" "236" "237" "238" "239" "240" "241" "242" "243" "244" "245" "246" "247" "248" "249" "250" "251" "252" "253" "254" "255" "256" "257" "258" "259" "260" "261" "262" "263"
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"SE60" 3.23166587791011 3.14976242212005 3.18563710899584 3.20362933582566 3.05591182844985 3.37455599380577 3.46767105532593 3.02996620454721 3.38573977471579 3.83340266765193 3.16548592458619 3.04780370898111 3.81116854878479 3.70807546493221 3.72870224666338 3.91775602194866 3.5569385807202 3.57992298106016 3.12961983763289 3.42700482643091 3.26398481325001 3.1391969945444 3.28796921108802 3.24820921693833 3.08345662855132 3.28385113969275 3.52566389364565 3.27885428967703 3.28186395264591 3.75729684559974 3.22003058124405 3.39324547292196 3.5241837730097 3.24926774350075 3.5029568866702 3.167453858066 3.66002860531818 3.45797529763174 3.26662344603336 3.21190866970288 3.16671139202417 3.06810814178645 3.09553472252638 3.35009249819514 3.26911657500263 3.05420590665584 3.18383478256835 3.10231876529181 3.08631224331267 3.32184092480967 2.9612548342392 3.11399036213895 3.27740489077092 3.05420590665584 3.28365634889956 3.07639389977073 3.2851180532263 3.00212445447505 3.02996620454721 3.0471824811232 3.38638844689011 3.05870400930041 3.63547947360773 3.12494979702456 3.30184961597097 2.99073837057165 3.46448533043147 3.173371030979 3.41376000370833 3.18987609510807 3.79341734659743 3.36875234430635 3.60243479166458 3.49781046206083 3.71750747921295 3.31205178101901 3.14526946575748 3.15910788349704 3.48104432565627 3.54328524409282 3.25515753573459 3.06556918831434 3.22573266753822 3.07910823127566 3.11622190652859 3.30698684877783 3.28589767837051 3.35065476116907 3.47058572855541 3.14810547109397 2.98299162687224 3.17010317436166 3.40586290187944 3.2262165736518 3.24808920307098 3.04780370898111 3.1788823935293 3.11399036213895 3.63510462314999 3.07182955512787 3.08007769237046 3.18966408921486 3.09365854180327 3.35447998690043 2.81295001947974 0.865216710367395 1.82739261142734 2.81295001947974 1.80481296146466 2.21316157561511 2.59194629047591 2.10377148342693 3.05480075523662 1.67651874727463 3.44880881230198 3.2497534080617 3.20235840706673 1.66199883530969 1.73571144163437 3.25515753573459 3.46791068038354 2.56081666965146 1.70742720095843 2.61501398432537 3.60379482574174 2.26609060824517 2.10377148342693 3.33041991062619 3.47092555588517 3.25582749318565 3.04651483914812 1.72430981271069 3.58199305315135 3.24667254601392 2.79024822755872 1.78256941391896 3.07639389977073 2.54867370578296 3.07998608240068 3.93033543239317 3.23298598365555 3.14472109166931 3.34987423777477 2.23517300967877 2.23731217473929 2.81714774581565 2.21316157561511 3.1761454304726 3.07695553511101 3.37780452724724 3.05079031826683 3.48633955818765 2.29067699282898 2.78829499268418 1.04978725442864 3.24244629727988 2.67393667812761 1.72868949257027 3.69596201759191 3.49420052708446 3.36536491351792 3.4499815024958 3.44384296036279 2.89595850715581 2.23298634729565 2.84932132116437 3.03715583706785 3.26960348217275 3.11227093139341 3.31148816967164 3.71000550085236 3.73192643313328 3.82256315255729 3.07695553511101 3.27405627028294 3.68670562716594 3.62585684347877 3.17578001071172 3.42525316422957 3.56489906086642 3.39389896137435 3.11227093139341 3.71099874330346 3.66017111519743 3.14395907118589 3.19111496648318 3.42130093981288 3.57372024426274 3.53345661800998 3.47961256866335 3.00958291918619 3.18797056138399 3.27500139952482 3.50504510732479 3.15958113886602 3.3300098035371 3.11399036213895 3.29316361582645 3.5424756542362 3.1377829133458 3.30787325317458 3.73837562507916 3.26911657500263 3.03882019497781 3.35709838439453 3.11072919627193 3.17299803817843 3.09000230219319 3.10927217332377 3.28894572696993 3.00893217396503 3.13771609701428 3.34923843518786 3.53265527255483 3.17251029614319 3.06893998732962 3.13578997025742 3.40344236925577 3.05192970257922 3.07056281773793 2.9612548342392 3.13771609701428 3.16371395474898 3.22003058124405 3.17341553828897 3.22447177758755 3.50098790905608 3.38224868285735 3.40192966663161 3.08485657678677 3.46324562746112 3.10144480826215 3.32308578850902 3.09553472252638 3.30608331232595 3.17803182704971 3.28720064335898 3.55225875125816 3.45112770673955 3.5744755257162 3.75237189991267 3.79433099100227 3.27781591675831 3.4552771363789 3.3905273440055 3.37976932581233 3.39711190141198 3.25697453266653 3.55044815985382 3.37289111561266 3.5851406964876 3.11072919627193 3.07585765691215 3.5637322198611 3.16264349567261 3.26511939453169 3.93335378693751 3.3101719822095 3.22423934617532 3.06931661335875 3.55033578818425 3.27777376811434 3.22028217669959
"KL80" 1.19336833917501 1.09386449786322 0.808042039401498 0.805400082144296 0.591890557043784 0.705985155032699 0.794264477142889 0.668112997625519 0.744112156678772 0.802705047307273 0.705985155032699 0.748852078693249 0.691462194123947 0.984075585637764 0.945954289477955 0.832591346815414 0.618936196125733 0.761290452841916 0.734841595278846 0.880880895283194 1.01263557681872 0.810436625551192 0.808042039401498 1.29538738235306 0.87389230550394 0.819823798842761 0.635813301085181 0.851900325054614 0.851900325054614 0.878052467433769 0.796953834370656 0.837752851977424 0.682628551605219 0.824835883003075 0.819394499532416 0.860236409662029 1.01788560661209 0.87815056482854 0.87815056482854 1.16628181213915 0.928969469978114 1.08556518461671 0.895024522609351 0.722227311332711 0.753606929043437 0.797491211839927 0.837752851977424 1.6011300428185 2.17587389241098 2.01401257899788 1.57624019925067 1.71426311227284 1.12365798545349 2.14052463023617 1.2915823013296 2.01401257899788 0.958004728332126 2.66993143937081 0.701889466205572 2.73214251113852 1.26571153078916 1.75082974722234 1.56565972178933 1.82800392666558 1.81460458717031 2.01401257899788 1.89912284379672 2.66993143937081 2.21269078453544 1.25325849520366 1.40577925258682 2.1447881647376 0.986211428614337 1.37945391560139 1.10267651011258 1.89912284379672 1.30510414141192 2.17587389241098 0.998399971018125 1.34613181883513 1.07604223656474 2.07311240038111 2.17587389241098 2.46744692209474 2.52256944231307 2.02542126652235 3.43898044726523 1.0073868188749 2.14330107797129 0.831901737575564 1.89912284379672 1.47728219586079 1.65612581742141 1.70416258148035 1.85205891982772 1.79074722031677 1.42840999215239 2.25104410043925 1.06187076794897 1.99144418984194 2.14052463023617 1.35297028194127 2.46744692209474 1.98194052618736 1.16140927337719 2.73214251113852 1.7474566910175 1.65612581742141 2.14052463023617 2.14052463023617 1.48145720696391 1.57624019925067 0.901179131485603 2.01401257899788 1.35546009879505 1.51009179050952 1.01518972189173 2.55501760270282 2.55501760270282 0.884543106957961 2.01082660938713 1.79074722031677 2.01401257899788 2.46744692209474 1.24336037381397 1.77843116096642 2.01401257899788 1.16628181213915 1.31942298910884 0.965638813742046 1.04253436851439 1.99104645726763 1.78684564781875 1.2007609806781 1.7808488827312 2.66993143937081 0.591890557043784 1.41664452108593 1.60576481647627 0.765053500583319 1.07733099036229 0.72249651969139 1.15629401437619 2.01401257899788 1.49853795640749 1.99104645726763 1.67468300246925 0.99430131527341 1.86952013502338 1.17754733866363 0.913554938005079 1.08139969324113 1.62708522936439 1.50615005347655 2.46744692209474 1.05827301666363 2.08174771964936 3.28405368612311 0.609350476141929 1.54312333544003 0.929215810156095 0.700404473401211 0.845491744132299 1.65612581742141 1.96599402950101 2.3330178151786 1.24506966917638 1.54086353779747 2.01401257899788 1.7808488827312 0.845648026452437 1.82800392666558 1.43341423475243 1.86952013502338 2.46744692209474 1.05606943625762 1.65612581742141 2.07311240038111 1.58313643335092 2.32388325112574 2.11132474866447 1.77843116096642 1.27899470857783 2.73214251113852 2.83593684759346 1.59913742730809 1.64303771691663 1.2373139647715 1.86990322071358 1.35485241050737 0.705985155032699 0.665730143301341 1.79074722031677 1.37659140889562 1.49408298761653 1.96599402950101 2.4422704689859 2.31315479029213 1.61516802210925 2.01401257899788 1.86952013502338 2.14052463023617 1.74085210090096 4.59651509530194 1.02523490298451 2.28059346420019 1.2373139647715 1.68270061745526 1.75752564027238 1.62242597926738 1.79074722031677 1.01476434094783 0.853121392339337 0.894884324838418 1.16628181213915 0.784271773783854 1.01788560661209 0.956274200843235 2.38830721955939 1.25567484271213 1.29973168582767 1.33176615716258 0.912852337441958 0.721816011888643 0.849242520160229 0.690009032804825 1.01684889408342 0.824835883003075 0.768786901912184 1.01788560661209 1.01788560661209 1.16628181213915 0.829947159234049 0.668112997625519 0.595568503742769 0.807892241728994 0.908035409557369 0.880012970697654 0.971088218400022 0.967544013868313 0.797793119832107 0.838895870588385 0.672462699277603 0.63925630130811 0.829822328264438 0.957776255108305 0.700166526709203 0.686482550479837 0.604462142294605 0.784742380247956 0.719949077634205 0.810436625551192 0.709234084124087 0.991704033341539 0.895024522609351 0.935460974855343 0.568594589903026 0.77554971827386 0.964660195734967 0.702029272205366 0.87815056482854 1.10531032688844 1.6778106478484
"SE80" 3.43043180779228 3.30673827901679 3.40022601054121 3.42670613205235 3.27160448355216 3.2630245728609 3.50670282527585 3.35681101292116 3.3936207734661 3.34042023642027 3.2630245728609 3.27737189088705 3.43569580096287 3.34583393095478 3.40660943560066 3.3682197194489 3.55722054214897 3.41218444111204 3.3304745079423 3.21839130332319 3.37326613494522 3.31665547770192 3.40022601054121 3.35587284787047 3.33781804834398 3.24221295638823 3.5136000416635 3.29968354617361 3.29968354617361 3.49108651753245 3.19204673907448 3.19295590168176 3.36747838809555 3.23331488159235 3.33255000233963 3.37308772971637 3.29782871926234 3.30922167105434 3.30922167105434 3.33931994087443 3.35216583612886 3.27127057526869 3.25712238411892 3.39915623467128 3.25430327901098 3.30961004586165 3.19295590168176 2.68111266499077 1.67695539311133 1.51616862428391 2.14745060224537 2.70431748332839 2.89154285566361 1.71672922091872 2.70485393276899 1.51616862428391 3.37001471572678 1.59942718364747 3.25416371876575 1.49401663873999 2.95276957464953 2.23764543123109 2.97734674546754 2.35443946802675 2.7121665838672 1.51616862428391 2.12962802343522 1.59942718364747 2.22383774487007 2.65151015777953 3.01020879793167 2.62476432558803 3.45844312522254 3.17569094536265 3.14111050031859 2.12962802343522 2.87288365592501 1.67695539311133 3.26233489955883 3.02100411556219 2.95825308070502 2.30176070694006 1.67695539311133 1.79947743386277 1.6967095747501 2.52939356893087 1.61082257212097 3.33789264515543 2.29201031790384 3.34925112496318 2.12962802343522 2.84353745628212 2.40596328613479 2.18085226113595 2.1982916839741 2.2345635805075 2.4097044989133 2.24214748145346 3.11906320493498 2.23903195363189 1.71672922091872 2.65934773178876 1.79947743386277 2.5730943125299 2.96700906222549 1.49401663873999 2.39705109860396 2.40596328613479 1.71672922091872 1.71672922091872 2.98198571208667 2.14745060224537 3.27282361325407 1.51616862428391 2.73461522985894 2.85264157805626 3.34436896442318 1.27632498188254 1.27632498188254 3.31651883821286 2.41560550392436 2.2345635805075 1.51616862428391 1.79947743386277 2.75684409310059 2.16911884165381 1.51616862428391 3.33931994087443 3.03824544428131 3.26456284180377 3.00066800903289 2.23167262620322 2.75554519211316 2.77569307056869 2.42563718467235 1.59942718364747 3.27160448355216 2.91500142164238 3.04281986699487 3.68524625566982 3.23545241805406 3.36335238381847 2.95578093322832 1.51616862428391 2.67813826646947 2.23167262620322 2.16961521540088 2.86715334993556 2.1974196845139 3.23139607896788 3.2580632871454 2.99061512156683 2.76505326848873 2.58611019703247 1.79947743386277 3.2977509690994 2.53372540762186 1.31964474966964 3.36744745690894 2.69950221219502 3.30361934081168 3.3744590731567 3.33232067310681 2.40596328613479 2.28110752143235 2.32656300602364 2.98022277291373 2.73951515999455 1.51616862428391 2.42563718467235 3.1370785035457 2.35443946802675 2.58361244484251 2.1974196845139 1.79947743386277 2.90492125768032 2.40596328613479 2.30176070694006 3.02181384839216 2.33159419392138 2.37698278999542 2.16911884165381 3.04505246483092 1.49401663873999 2.25524488710105 2.64554643396442 2.39522871719241 2.7414334640804 2.31598024038642 2.73441281644665 3.2630245728609 3.36140758898075 2.2345635805075 2.71671773041242 2.67164521984289 2.28110752143235 2.25697349883849 2.32443375544792 2.66456946099332 1.51616862428391 2.1974196845139 1.71672922091872 2.24784308081652 1.31648975106882 2.86958306585253 1.63660693551009 2.7414334640804 2.35679360024515 2.44874042386712 2.37922483573487 2.2345635805075 2.93732317835719 3.27386589358977 3.1687991316637 3.33931994087443 3.22990189857453 3.29782871926234 3.36970288611539 2.09192872904855 2.7163509786486 2.46700527701046 2.65340744007001 2.87114217224112 3.15244242782219 3.23332923960429 3.37684186911695 3.2682437168226 3.23331488159235 3.40262156693197 3.29782871926234 3.29782871926234 3.33931994087443 3.25306352462535 3.35681101292116 3.35764967285971 3.40019217302331 3.27263517903996 3.43243071025426 3.44256915494088 3.28510997795291 3.42244657632028 3.47850136198892 3.34071089297889 3.43755821316595 3.49315996945863 3.25645808020333 3.38234576379265 3.42575392422634 3.75089490549789 3.4107643566256 3.35299408966905 3.31665547770192 3.32408389944884 3.41003813283345 3.25712238411892 3.38520167713715 3.57455341926173 3.29124187953913 3.2658361647626 3.35510122965464 3.30922167105434 3.35902325968741 3.37787113567494
tests/BLAT_jet.res deleted 100644 → 0
AA pos chain pc tr freq trace
HIS 1 A 0.5972 0.0 0.0 0.0
PRO 2 A 0.466 0.0 0.0 0.0
GLU 3 A 0.3348 0.0 0.0 0.0
THR 4 A 0.3257 0.4347 0.0232 0.0101
LEU 5 A 0.7058 0.2588 0.0697 0.018
VAL 6 A 0.5656 0.3442 0.1627 0.056
LYS 7 A 0.2488 0.2908 0.7441 0.2164
VAL 8 A 0.5656 0.4946 1.0 0.4946
LYS 9 A 0.2488 0.3997 0.7906 0.316
ASP 10 A 0.3212 0.3727 0.3255 0.1213
ALA 11 A 0.3846 0.626 0.9767 0.6114
GLU 12 A 0.3348 0.72 1.0 0.72
ASP 13 A 0.3212 0.3092 0.7674 0.2373
GLN 14 A 0.4343 0.325 0.9302 0.3023
LEU 15 A 0.7058 0.3874 0.9767 0.3784
GLY 16 A 0.4117 0.5288 0.9767 0.5165
ALA 17 A 0.3846 0.7106 1.0 0.7106
ARG 18 A 0.5067 0.6703 1.0 0.6703
VAL 19 A 0.5656 0.6373 1.0 0.6373
GLY 20 A 0.4117 0.8195 1.0 0.8195
TYR 21 A 0.7963 0.6647 1.0 0.6647
ILE 22 A 0.638 0.5084 0.9767 0.4966
GLU 23 A 0.3348 0.5795 1.0 0.5795
LEU 24 A 0.7058 0.4498 1.0 0.4498
ASP 25 A 0.3212 0.674 1.0 0.674
LEU 26 A 0.7058 0.6364 1.0 0.6364
ASN 27 A 0.3936 0.4363 0.9069 0.3957
SER 28 A 0.3574 0.5123 0.9534 0.4884
GLY 29 A 0.4117 0.5862 0.9767 0.5726
LYS 30 A 0.2488 0.3089 0.9069 0.2802
ILE 31 A 0.638 0.3236 0.9302 0.301
LEU 32 A 0.7058 0.4179 0.9534 0.3984
GLU 33 A 0.3348 0.2014 0.5116 0.103
SER 34 A 0.3574 0.3545 0.9069 0.3215
PHE 35 A 1.0 0.4728 0.9302 0.4398
ARG 36 A 0.5067 0.7055 1.0 0.7055
PRO 37 A 0.466 0.4524 0.9534 0.4314
GLU 38 A 0.3348 0.4643 0.9069 0.4211
GLU 39 A 0.3348 0.6633 1.0 0.6633
ARG 40 A 0.5067 0.6755 1.0 0.6755
PHE 41 A 1.0 0.7719 1.0 0.7719
PRO 42 A 0.466 0.6902 1.0 0.6902
MET 43 A 0.6606 0.5544 1.0 0.5544
MET 44 A 0.6606 0.7353 1.0 0.7353
SER 45 A 0.3574 0.9044 1.0 0.9044
THR 46 A 0.3257 0.7685 1.0 0.7685
PHE 47 A 1.0 0.6929 1.0 0.6929
LYS 48 A 0.2488 0.9136 1.0 0.9136
VAL 49 A 0.5656 0.4874 1.0 0.4874
LEU 50 A 0.7058 0.6097 1.0 0.6097
LEU 51 A 0.7058 0.6193 1.0 0.6193
CYS 52 A 0.6425 0.6526 1.0 0.6526
GLY 53 A 0.4117 0.6031 1.0 0.6031
ALA 54 A 0.3846 0.6007 1.0 0.6007
VAL 55 A 0.5656 0.5982 0.9767 0.5843
LEU 56 A 0.7058 0.8401 1.0 0.8401
SER 57 A 0.3574 0.4586 1.0 0.4586
ARG 58 A 0.5067 0.5235 1.0 0.5235
VAL 59 A 0.5656 0.5751 1.0 0.5751
ASP 60 A 0.3212 0.6858 1.0 0.6858
ALA 61 A 0.3846 0.3795 0.9069 0.3442
GLY 62 A 0.4117 0.8186 1.0 0.8186
GLN 63 A 0.4343 0.3198 0.8837 0.2826
GLU 64 A 0.3348 0.5645 0.9767 0.5514
GLN 65 A 0.4343 0.4432 0.9534 0.4226
LEU 66 A 0.7058 0.8349 1.0 0.8349
GLY 67 A 0.4117 0.3756 0.8837 0.3319
ARG 68 A 0.5067 0.5446 1.0 0.5446
ARG 69 A 0.5067 0.4885 0.9767 0.4771
ILE 70 A 0.638 0.5203 1.0 0.5203
HIS 71 A 0.5972 0.2709 0.9069 0.2457
TYR 72 A 0.7963 0.5582 1.0 0.5582
SER 73 A 0.3574 0.326 0.9534 0.3108
GLN 74 A 0.4343 0.3766 0.9534 0.3591
ASN 75 A 0.3936 0.3075 0.9069 0.2789
ASP 76 A 0.3212 0.6403 1.0 0.6403
LEU 77 A 0.7058 0.6112 1.0 0.6112
VAL 78 A 0.5656 0.5734 1.0 0.5734
GLU 79 A 0.3348 0.3159 0.8139 0.2571
TYR 80 A 0.7963 0.6077 1.0 0.6077
SER 81 A 0.3574 0.7039 1.0 0.7039
PRO 82 A 0.466 0.8559 1.0 0.8559
VAL 83 A 0.5656 0.5439 1.0 0.5439
THR 84 A 0.3257 0.6013 0.9767 0.5873
GLU 85 A 0.3348 0.5533 1.0 0.5533
LYS 86 A 0.2488 0.5085 1.0 0.5085
HIS 87 A 0.5972 0.6068 1.0 0.6068
LEU 88 A 0.7058 0.5502 0.9767 0.5374
THR 89 A 0.3257 0.4525 1.0 0.4525
ASP 90 A 0.3212 0.4788 0.9767 0.4677
GLY 91 A 0.4117 0.5906 1.0 0.5906
MET 92 A 0.6606 0.6702 1.0 0.6702
THR 93 A 0.3257 0.6015 1.0 0.6015
VAL 94 A 0.5656 0.5133 1.0 0.5133
ARG 95 A 0.5067 0.402 0.9302 0.3739
GLU 96 A 0.3348 0.5729 1.0 0.5729
LEU 97 A 0.7058 0.7637 1.0 0.7637
CYS 98 A 0.6425 0.7754 1.0 0.7754
SER 99 A 0.3574 0.4087 1.0 0.4087
ALA 100 A 0.3846 0.8239 1.0 0.8239
ALA 101 A 0.3846 0.6841 1.0 0.6841
ILE 102 A 0.638 0.5323 0.9534 0.5075
THR 103 A 0.3257 0.6462 1.0 0.6462
MET 104 A 0.6606 0.4679 1.0 0.4679
SER 105 A 0.3574 0.9398 1.0 0.9398
ASP 106 A 0.3212 0.9667 1.0 0.9667
ASN 107 A 0.3936 0.8815 1.0 0.8815
THR 108 A 0.3257 0.6407 1.0 0.6407
ALA 109 A 0.3846 0.892 1.0 0.892
ALA 110 A 0.3846 0.6346 1.0 0.6346
ASN 111 A 0.3936 0.9217 1.0 0.9217
LEU 112 A 0.7058 0.6879 1.0 0.6879
LEU 113 A 0.7058 0.8471 1.0 0.8471
LEU 114 A 0.7058 0.7508 1.0 0.7508
THR 115 A 0.3257 0.33 0.9767 0.3224
THR 116 A 0.3257 0.444 0.9069 0.4027
ILE 117 A 0.638 0.4587 1.0 0.4587
GLY 118 A 0.4117 0.9119 1.0 0.9119
GLY 119 A 0.4117 0.916 1.0 0.916
PRO 120 A 0.466 0.8286 1.0 0.8286
LYS 121 A 0.2488 0.4039 0.9302 0.3757
GLU 122 A 0.3348 0.5031 1.0 0.5031
LEU 123 A 0.7058 0.7041 1.0 0.7041
THR 124 A 0.3257 0.77 1.0 0.77
ALA 125 A 0.3846 0.4784 1.0 0.4784
PHE 126 A 1.0 0.6642 1.0 0.6642
LEU 127 A 0.7058 0.6359 1.0 0.6359
HIS 128 A 0.5972 0.6663 1.0 0.6663
ASN 129 A 0.3936 0.3287 1.0 0.3287
MET 130 A 0.6606 0.4932 0.9767 0.4817
GLY 131 A 0.4117 0.8933 1.0 0.8933
ASP 132 A 0.3212 0.8796 1.0 0.8796
HIS 133 A 0.5972 0.2495 0.9767 0.2437
VAL 134 A 0.5656 0.4522 1.0 0.4522
THR 135 A 0.3257 0.7187 1.0 0.7187
ARG 136 A 0.5067 0.7525 1.0 0.7525
LEU 137 A 0.7058 0.7365 1.0 0.7365
ASP 138 A 0.3212 0.7821 1.0 0.7821
ARG 139 A 0.5067 0.7324 1.0 0.7324
TRP 140 A 0.9909 0.4071 1.0 0.4071
GLU 141 A 0.3348 0.8613 1.0 0.8613
PRO 142 A 0.466 0.6335 1.0 0.6335
GLU 143 A 0.3348 0.4561 0.9302 0.4242
LEU 144 A 0.7058 0.7899 1.0 0.7899
ASN 145 A 0.3936 0.8108 1.0 0.8108
GLU 146 A 0.3348 0.5191 1.0 0.5191
ALA 147 A 0.3846 0.6269 1.0 0.6269
ILE 148 A 0.638 0.3016 0.9302 0.2805
PRO 149 A 0.466 0.6968 1.0 0.6968
ASN 150 A 0.3936 0.617 1.0 0.617
ASP 151 A 0.3212 0.7192 1.0 0.7192
GLU 152 A 0.3348 0.453 1.0 0.453
ARG 153 A 0.5067 0.7487 1.0 0.7487
ASP 154 A 0.3212 0.9192 1.0 0.9192
THR 155 A 0.3257 0.868 1.0 0.868
THR 156 A 0.3257 0.781 1.0 0.781
MET 157 A 0.6606 0.6942 1.0 0.6942
PRO 158 A 0.466 0.8649 1.0 0.8649
ALA 159 A 0.3846 0.3886 0.9534 0.3705
ALA 160 A 0.3846 0.7373 1.0 0.7373
MET 161 A 0.6606 0.6553 0.9767 0.64
ALA 162 A 0.3846 0.5496 1.0 0.5496
THR 163 A 0.3257 0.3432 0.8837 0.3033
THR 164 A 0.3257 0.6051 1.0 0.6051
LEU 165 A 0.7058 0.7829 1.0 0.7829
ARG 166 A 0.5067 0.4037 1.0 0.4037
LYS 167 A 0.2488 0.3098 0.9069 0.2809
LEU 168 A 0.7058 0.6868 1.0 0.6868
LEU 169 A 0.7058 0.4621 1.0 0.4621
THR 170 A 0.3257 0.5794 1.0 0.5794
GLY 171 A 0.4117 0.7193 1.0 0.7193
GLU 172 A 0.3348 0.3758 0.9302 0.3496
LEU 173 A 0.7058 0.4917 0.9302 0.4574
LEU 174 A 0.7058 0.869 1.0 0.869
THR 175 A 0.3257 0.4844 1.0 0.4844
LEU 176 A 0.7058 0.3332 0.8837 0.2944
ALA 177 A 0.3846 0.3386 0.9767 0.3307
SER 178 A 0.3574 0.7089 1.0 0.7089
ARG 179 A 0.5067 0.6869 1.0 0.6869
GLN 180 A 0.4343 0.3558 0.8372 0.2979
GLN 181 A 0.4343 0.5421 1.0 0.5421
LEU 182 A 0.7058 0.7735 1.0 0.7735
ILE 183 A 0.638 0.3582 0.9302 0.3332
ASP 184 A 0.3212 0.3176 0.9534 0.3028
TRP 185 A 0.9909 0.7627 1.0 0.7627
MET 186 A 0.6606 0.6868 1.0 0.6868
GLU 187 A 0.3348 0.3563 1.0 0.3563
ALA 188 A 0.3846 0.4534 0.9767 0.4429
ASP 189 A 0.3212 0.6211 1.0 0.6211
LYS 190 A 0.2488 0.4287 0.9767 0.4187
VAL 191 A 0.5656 0.7194 1.0 0.7194
ALA 192 A 0.3846 0.7564 1.0 0.7564
GLY 193 A 0.4117 0.444 0.9767 0.4337
PRO 194 A 0.466 0.3414 1.0 0.3414
LEU 195 A 0.7058 0.6718 1.0 0.6718
LEU 196 A 0.7058 0.7407 1.0 0.7407
ARG 197 A 0.5067 0.7398 1.0 0.7398
SER 198 A 0.3574 0.7212 1.0 0.7212
ALA 199 A 0.3846 0.6839 1.0 0.6839
LEU 200 A 0.7058 0.7322 1.0 0.7322
PRO 201 A 0.466 0.797 1.0 0.797
ALA 202 A 0.3846 0.3421 0.7209 0.2466
GLY 203 A 0.4117 0.4785 0.9767 0.4674
TRP 204 A 0.9909 0.7825 1.0 0.7825
PHE 205 A 1.0 0.3438 0.8837 0.3039
ILE 206 A 0.638 0.6603 1.0 0.6603
ALA 207 A 0.3846 0.6971 1.0 0.6971
ASP 208 A 0.3212 0.8033 1.0 0.8033
LYS 209 A 0.2488 0.8689 1.0 0.8689
SER 210 A 0.3574 0.8046 1.0 0.8046
GLY 211 A 0.4117 0.9153 1.0 0.9153
ALA 212 A 0.3846 0.6087 1.0 0.6087
GLY 213 A 0.4117 0.641 1.0 0.641
GLU 214 A 0.3348 0.3573 0.8604 0.3074
ARG 215 A 0.5067 0.5351 0.9767 0.5226
GLY 216 A 0.4117 0.6814 1.0 0.6814
SER 217 A 0.3574 0.5287 1.0 0.5287
ARG 218 A 0.5067 0.5215 1.0 0.5215
GLY 219 A 0.4117 0.7282 1.0 0.7282
ILE 220 A 0.638 0.8036 1.0 0.8036
ILE 221 A 0.638 0.4852 1.0 0.4852
ALA 222 A 0.3846 0.7583 1.0 0.7583
ALA 223 A 0.3846 0.5302 1.0 0.5302
LEU 224 A 0.7058 0.4201 0.9302 0.3908
GLY 225 A 0.4117 0.6237 1.0 0.6237
PRO 226 A 0.466 0.6749 1.0 0.6749
ASP 227 A 0.3212 0.6761 0.9534 0.6447
GLY 228 A 0.4117 0.3815 0.6976 0.2662
LYS 229 A 0.2488 0.6132 0.9534 0.5847
PRO 230 A 0.466 0.4194 0.8604 0.3609
SER 231 A 0.3574 0.6727 1.0 0.6727
ARG 232 A 0.5067 0.4888 1.0 0.4888
ILE 233 A 0.638 0.5329 1.0 0.5329
VAL 234 A 0.5656 0.4653 0.9069 0.422
VAL 235 A 0.5656 0.5177 0.9534 0.4936
ILE 236 A 0.638 0.5614 0.9767 0.5484
TYR 237 A 0.7963 0.6596 1.0 0.6596
THR 238 A 0.3257 0.5316 0.9767 0.5192
THR 239 A 0.3257 0.4994 1.0 0.4994
GLY 240 A 0.4117 0.4444 0.9302 0.4134
SER 241 A 0.3574 0.4848 0.8837 0.4284
GLN 242 A 0.4343 0.2784 0.6976 0.1942
ALA 243 A 0.3846 0.415 0.8837 0.3668
THR 244 A 0.3257 0.4881 0.9302 0.4541
MET 245 A 0.6606 0.4663 0.9302 0.4338
ASP 246 A 0.3212 0.286 0.6511 0.1862
GLU 247 A 0.3348 0.2998 0.7441 0.2231
ARG 248 A 0.5067 0.5129 0.9302 0.4772
ASN 249 A 0.3936 0.3689 0.9069 0.3346
ARG 250 A 0.5067 0.4898 0.9069 0.4443
GLN 251 A 0.4343 0.5672 1.0 0.5672
ILE 252 A 0.638 0.6216 0.9767 0.6071
ALA 253 A 0.3846 0.68 1.0 0.68
GLU 254 A 0.3348 0.3688 0.6744 0.2487
ILE 255 A 0.638 0.5916 0.9767 0.5778
GLY 256 A 0.4117 0.5344 0.9069 0.4847
ALA 257 A 0.3846 0.5051 0.8604 0.4346
SER 258 A 0.3574 0.4544 0.9069 0.4121
LEU 259 A 0.7058 0.4646 0.8372 0.389
ILE 260 A 0.638 0.4682 0.6279 0.294
LYS 261 A 0.2488 0.3211 0.0697 0.0224
HIS 262 A 0.5972 0.0555 0.0232 0.0012
TRP 263 A 0.9909 0.0555 0.0232 0.0012
tests/BLAT_normPred_evolCombi.txt deleted 100644 → 0
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tests/BLAT_normPred_evolEpi.txt deleted 100644 → 0
"V1" "V2" "V3" "V4" "V5" "V6" "V7" "V8" "V9" "V10" "V11" "V12" "V13" "V14" "V15" "V16" "V17" "V18" "V19" "V20" "V21" "V22" "V23" "V24" "V25" "V26" "V27" "V28" "V29" "V30" "V31" "V32" "V33" "V34" "V35" "V36" "V37" "V38" "V39" "V40" "V41" "V42" "V43" "V44" "V45" "V46" "V47" "V48" "V49" "V50" "V51" "V52" "V53" "V54" "V55" "V56" "V57" "V58" "V59" "V60" "V61" "V62" "V63" "V64" "V65" "V66" "V67" "V68" "V69" "V70" "V71" "V72" "V73" "V74" "V75" "V76" "V77" "V78" "V79" "V80" "V81" "V82" "V83" "V84" "V85" "V86" "V87" "V88" "V89" "V90" "V91" "V92" "V93" "V94" "V95" "V96" "V97" "V98" "V99" "V100" "V101" "V102" "V103" "V104" "V105" "V106" "V107" "V108" "V109" "V110" "V111" "V112" "V113" "V114" "V115" "V116" "V117" "V118" "V119" "V120" "V121" "V122" "V123" "V124" "V125" "V126" "V127" "V128" "V129" "V130" "V131" "V132" "V133" "V134" "V135" "V136" "V137" "V138" "V139" "V140" "V141" "V142" "V143" "V144" "V145" "V146" "V147" "V148" "V149" "V150" "V151" "V152" "V153" "V154" "V155" "V156" "V157" "V158" "V159" "V160" "V161" "V162" "V163" "V164" "V165" "V166" "V167" "V168" "V169" "V170" "V171" "V172" "V173" "V174" "V175" "V176" "V177" "V178" "V179" "V180" "V181" "V182" "V183" "V184" "V185" "V186" "V187" "V188" "V189" "V190" "V191" "V192" "V193" "V194" "V195" "V196" "V197" "V198" "V199" "V200" "V201" "V202" "V203" "V204" "V205" "V206" "V207" "V208" "V209" "V210" "V211" "V212" "V213" "V214" "V215" "V216" "V217" "V218" "V219" "V220" "V221" "V222" "V223" "V224" "V225" "V226" "V227" "V228" "V229" "V230" "V231" "V232" "V233" "V234" "V235" "V236" "V237" "V238" "V239" "V240" "V241" "V242" "V243" "V244" "V245" "V246" "V247" "V248" "V249" "V250" "V251" "V252" "V253" "V254" "V255" "V256" "V257" "V258" "V259" "V260" "V261" "V262" "V263"
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tests/BLAT_normPred_evolInd.txt deleted 100644 → 0
"V1" "V2" "V3" "V4" "V5" "V6" "V7" "V8" "V9" "V10" "V11" "V12" "V13" "V14" "V15" "V16" "V17" "V18" "V19" "V20" "V21" "V22" "V23" "V24" "V25" "V26" "V27" "V28" "V29" "V30" "V31" "V32" "V33" "V34" "V35" "V36" "V37" "V38" "V39" "V40" "V41" "V42" "V43" "V44" "V45" "V46" "V47" "V48" "V49" "V50" "V51" "V52" "V53" "V54" "V55" "V56" "V57" "V58" "V59" "V60" "V61" "V62" "V63" "V64" "V65" "V66" "V67" "V68" "V69" "V70" "V71" "V72" "V73" "V74" "V75" "V76" "V77" "V78" "V79" "V80" "V81" "V82" "V83" "V84" "V85" "V86" "V87" "V88" "V89" "V90" "V91" "V92" "V93" "V94" "V95" "V96" "V97" "V98" "V99" "V100" "V101" "V102" "V103" "V104" "V105" "V106" "V107" "V108" "V109" "V110" "V111" "V112" "V113" "V114" "V115" "V116" "V117" "V118" "V119" "V120" "V121" "V122" "V123" "V124" "V125" "V126" "V127" "V128" "V129" "V130" "V131" "V132" "V133" "V134" "V135" "V136" "V137" "V138" "V139" "V140" "V141" "V142" "V143" "V144" "V145" "V146" "V147" "V148" "V149" "V150" "V151" "V152" "V153" "V154" "V155" "V156" "V157" "V158" "V159" "V160" "V161" "V162" "V163" "V164" "V165" "V166" "V167" "V168" "V169" "V170" "V171" "V172" "V173" "V174" "V175" "V176" "V177" "V178" "V179" "V180" "V181" "V182" "V183" "V184" "V185" "V186" "V187" "V188" "V189" "V190" "V191" "V192" "V193" "V194" "V195" "V196" "V197" "V198" "V199" "V200" "V201" "V202" "V203" "V204" "V205" "V206" "V207" "V208" "V209" "V210" "V211" "V212" "V213" "V214" "V215" "V216" "V217" "V218" "V219" "V220" "V221" "V222" "V223" "V224" "V225" "V226" "V227" "V228" "V229" "V230" "V231" "V232" "V233" "V234" "V235" "V236" "V237" "V238" "V239" "V240" "V241" "V242" "V243" "V244" "V245" "V246" "V247" "V248" "V249" "V250" "V251" "V252" "V253" "V254" "V255" "V256" "V257" "V258" "V259" "V260" "V261" "V262" "V263"
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tests/BLAT_pred_evolEpi.txt deleted 100644 → 0
"V1" "V2" "V3" "V4" "V5" "V6" "V7" "V8" "V9" "V10" "V11" "V12" "V13" "V14" "V15" "V16" "V17" "V18" "V19" "V20" "V21" "V22" "V23" "V24" "V25" "V26" "V27" "V28" "V29" "V30" "V31" "V32" "V33" "V34" "V35" "V36" "V37" "V38" "V39" "V40" "V41" "V42" "V43" "V44" "V45" "V46" "V47" "V48" "V49" "V50" "V51" "V52" "V53" "V54" "V55" "V56" "V57" "V58" "V59" "V60" "V61" "V62" "V63" "V64" "V65" "V66" "V67" "V68" "V69" "V70" "V71" "V72" "V73" "V74" "V75" "V76" "V77" "V78" "V79" "V80" "V81" "V82" "V83" "V84" "V85" "V86" "V87" "V88" "V89" "V90" "V91" "V92" "V93" "V94" "V95" "V96" "V97" "V98" "V99" "V100" "V101" "V102" "V103" "V104" "V105" "V106" "V107" "V108" "V109" "V110" "V111" "V112" "V113" "V114" "V115" "V116" "V117" "V118" "V119" "V120" "V121" "V122" "V123" "V124" "V125" "V126" "V127" "V128" "V129" "V130" "V131" "V132" "V133" "V134" "V135" "V136" "V137" "V138" "V139" "V140" "V141" "V142" "V143" "V144" "V145" "V146" "V147" "V148" "V149" "V150" "V151" "V152" "V153" "V154" "V155" "V156" "V157" "V158" "V159" "V160" "V161" "V162" "V163" "V164" "V165" "V166" "V167" "V168" "V169" "V170" "V171" "V172" "V173" "V174" "V175" "V176" "V177" "V178" "V179" "V180" "V181" "V182" "V183" "V184" "V185" "V186" "V187" "V188" "V189" "V190" "V191" "V192" "V193" "V194" "V195" "V196" "V197" "V198" "V199" "V200" "V201" "V202" "V203" "V204" "V205" "V206" "V207" "V208" "V209" "V210" "V211" "V212" "V213" "V214" "V215" "V216" "V217" "V218" "V219" "V220" "V221" "V222" "V223" "V224" "V225" "V226" "V227" "V228" "V229" "V230" "V231" "V232" "V233" "V234" "V235" "V236" "V237" "V238" "V239" "V240" "V241" "V242" "V243" "V244" "V245" "V246" "V247" "V248" "V249" "V250" "V251" "V252" "V253" "V254" "V255" "V256" "V257" "V258" "V259" "V260" "V261" "V262" "V263"
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tests/BLAT_pred_evolInd.txt deleted 100644 → 0
"V1" "V2" "V3" "V4" "V5" "V6" "V7" "V8" "V9" "V10" "V11" "V12" "V13" "V14" "V15" "V16" "V17" "V18" "V19" "V20" "V21" "V22" "V23" "V24" "V25" "V26" "V27" "V28" "V29" "V30" "V31" "V32" "V33" "V34" "V35" "V36" "V37" "V38" "V39" "V40" "V41" "V42" "V43" "V44" "V45" "V46" "V47" "V48" "V49" "V50" "V51" "V52" "V53" "V54" "V55" "V56" "V57" "V58" "V59" "V60" "V61" "V62" "V63" "V64" "V65" "V66" "V67" "V68" "V69" "V70" "V71" "V72" "V73" "V74" "V75" "V76" "V77" "V78" "V79" "V80" "V81" "V82" "V83" "V84" "V85" "V86" "V87" "V88" "V89" "V90" "V91" "V92" "V93" "V94" "V95" "V96" "V97" "V98" "V99" "V100" "V101" "V102" "V103" "V104" "V105" "V106" "V107" "V108" "V109" "V110" "V111" "V112" "V113" "V114" "V115" "V116" "V117" "V118" "V119" "V120" "V121" "V122" "V123" "V124" "V125" "V126" "V127" "V128" "V129" "V130" "V131" "V132" "V133" "V134" "V135" "V136" "V137" "V138" "V139" "V140" "V141" "V142" "V143" "V144" "V145" "V146" "V147" "V148" "V149" "V150" "V151" "V152" "V153" "V154" "V155" "V156" "V157" "V158" "V159" "V160" "V161" "V162" "V163" "V164" "V165" "V166" "V167" "V168" "V169" "V170" "V171" "V172" "V173" "V174" "V175" "V176" "V177" "V178" "V179" "V180" "V181" "V182" "V183" "V184" "V185" "V186" "V187" "V188" "V189" "V190" "V191" "V192" "V193" "V194" "V195" "V196" "V197" "V198" "V199" "V200" "V201" "V202" "V203" "V204" "V205" "V206" "V207" "V208" "V209" "V210" "V211" "V212" "V213" "V214" "V215" "V216" "V217" "V218" "V219" "V220" "V221" "V222" "V223" "V224" "V225" "V226" "V227" "V228" "V229" "V230" "V231" "V232" "V233" "V234" "V235" "V236" "V237" "V238" "V239" "V240" "V241" "V242" "V243" "V244" "V245" "V246" "V247" "V248" "V249" "V250" "V251" "V252" "V253" "V254" "V255" "V256" "V257" "V258" "V259" "V260" "V261" "V262" "V263"
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tests/BLAT_pssm.txt deleted 100644 → 0
"V1" "V2" "V3" "V4" "V5" "V6" "V7" "V8" "V9" "V10" "V11" "V12" "V13" "V14" "V15" "V16" "V17" "V18" "V19" "V20" "V21" "V22" "V23" "V24" "V25" "V26" "V27" "V28" "V29" "V30" "V31" "V32" "V33" "V34" "V35" "V36" "V37" "V38" "V39" "V40" "V41" "V42" "V43" "V44" "V45" "V46" "V47" "V48" "V49" "V50" "V51" "V52" "V53" "V54" "V55" "V56" "V57" "V58" "V59" "V60" "V61" "V62" "V63" "V64" "V65" "V66" "V67" "V68" "V69" "V70" "V71" "V72" "V73" "V74" "V75" "V76" "V77" "V78" "V79" "V80" "V81" "V82" "V83" "V84" "V85" "V86" "V87" "V88" "V89" "V90" "V91" "V92" "V93" "V94" "V95" "V96" "V97" "V98" "V99" "V100" "V101" "V102" "V103" "V104" "V105" "V106" "V107" "V108" "V109" "V110" "V111" "V112" "V113" "V114" "V115" "V116" "V117" "V118" "V119" "V120" "V121" "V122" "V123" "V124" "V125" "V126" "V127" "V128" "V129" "V130" "V131" "V132" "V133" "V134" "V135" "V136" "V137" "V138" "V139" "V140" "V141" "V142" "V143" "V144" "V145" "V146" "V147" "V148" "V149" "V150" "V151" "V152" "V153" "V154" "V155" "V156" "V157" "V158" "V159" "V160" "V161" "V162" "V163" "V164" "V165" "V166" "V167" "V168" "V169" "V170" "V171" "V172" "V173" "V174" "V175" "V176" "V177" "V178" "V179" "V180" "V181" "V182" "V183" "V184" "V185" "V186" "V187" "V188" "V189" "V190" "V191" "V192" "V193" "V194" "V195" "V196" "V197" "V198" "V199" "V200" "V201" "V202" "V203" "V204" "V205" "V206" "V207" "V208" "V209" "V210" "V211" "V212" "V213" "V214" "V215" "V216" "V217" "V218" "V219" "V220" "V221" "V222" "V223" "V224" "V225" "V226" "V227" "V228" "V229" "V230" "V231" "V232" "V233" "V234" "V235" "V236" "V237" "V238" "V239" "V240" "V241" "V242" "V243" "V244" "V245" "V246" "V247" "V248" "V249" "V250" "V251" "V252" "V253" "V254" "V255" "V256" "V257" "V258" "V259" "V260" "V261" "V262" "V263"
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tests/BLAT_pssm60.txt deleted 100644 → 0
"V1" "V2" "V3" "V4" "V5" "V6" "V7" "V8" "V9" "V10" "V11" "V12" "V13" "V14" "V15" "V16" "V17" "V18" "V19" "V20" "V21" "V22" "V23" "V24" "V25" "V26" "V27" "V28" "V29" "V30" "V31" "V32" "V33" "V34" "V35" "V36" "V37" "V38" "V39" "V40" "V41" "V42" "V43" "V44" "V45" "V46" "V47" "V48" "V49" "V50" "V51" "V52" "V53" "V54" "V55" "V56" "V57" "V58" "V59" "V60" "V61" "V62" "V63" "V64" "V65" "V66" "V67" "V68" "V69" "V70" "V71" "V72" "V73" "V74" "V75" "V76" "V77" "V78" "V79" "V80" "V81" "V82" "V83" "V84" "V85" "V86" "V87" "V88" "V89" "V90" "V91" "V92" "V93" "V94" "V95" "V96" "V97" "V98" "V99" "V100" "V101" "V102" "V103" "V104" "V105" "V106" "V107" "V108" "V109" "V110" "V111" "V112" "V113" "V114" "V115" "V116" "V117" "V118" "V119" "V120" "V121" "V122" "V123" "V124" "V125" "V126" "V127" "V128" "V129" "V130" "V131" "V132" "V133" "V134" "V135" "V136" "V137" "V138" "V139" "V140" "V141" "V142" "V143" "V144" "V145" "V146" "V147" "V148" "V149" "V150" "V151" "V152" "V153" "V154" "V155" "V156" "V157" "V158" "V159" "V160" "V161" "V162" "V163" "V164" "V165" "V166" "V167" "V168" "V169" "V170" "V171" "V172" "V173" "V174" "V175" "V176" "V177" "V178" "V179" "V180" "V181" "V182" "V183" "V184" "V185" "V186" "V187" "V188" "V189" "V190" "V191" "V192" "V193" "V194" "V195" "V196" "V197" "V198" "V199" "V200" "V201" "V202" "V203" "V204" "V205" "V206" "V207" "V208" "V209" "V210" "V211" "V212" "V213" "V214" "V215" "V216" "V217" "V218" "V219" "V220" "V221" "V222" "V223" "V224" "V225" "V226" "V227" "V228" "V229" "V230" "V231" "V232" "V233" "V234" "V235" "V236" "V237" "V238" "V239" "V240" "V241" "V242" "V243" "V244" "V245" "V246" "V247" "V248" "V249" "V250" "V251" "V252" "V253" "V254" "V255" "V256" "V257" "V258" "V259" "V260" "V261" "V262" "V263"
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tests/BLAT_pssm80.txt deleted 100644 → 0
"V1" "V2" "V3" "V4" "V5" "V6" "V7" "V8" "V9" "V10" "V11" "V12" "V13" "V14" "V15" "V16" "V17" "V18" "V19" "V20" "V21" "V22" "V23" "V24" "V25" "V26" "V27" "V28" "V29" "V30" "V31" "V32" "V33" "V34" "V35" "V36" "V37" "V38" "V39" "V40" "V41" "V42" "V43" "V44" "V45" "V46" "V47" "V48" "V49" "V50" "V51" "V52" "V53" "V54" "V55" "V56" "V57" "V58" "V59" "V60" "V61" "V62" "V63" "V64" "V65" "V66" "V67" "V68" "V69" "V70" "V71" "V72" "V73" "V74" "V75" "V76" "V77" "V78" "V79" "V80" "V81" "V82" "V83" "V84" "V85" "V86" "V87" "V88" "V89" "V90" "V91" "V92" "V93" "V94" "V95" "V96" "V97" "V98" "V99" "V100" "V101" "V102" "V103" "V104" "V105" "V106" "V107" "V108" "V109" "V110" "V111" "V112" "V113" "V114" "V115" "V116" "V117" "V118" "V119" "V120" "V121" "V122" "V123" "V124" "V125" "V126" "V127" "V128" "V129" "V130" "V131" "V132" "V133" "V134" "V135" "V136" "V137" "V138" "V139" "V140" "V141" "V142" "V143" "V144" "V145" "V146" "V147" "V148" "V149" "V150" "V151" "V152" "V153" "V154" "V155" "V156" "V157" "V158" "V159" "V160" "V161" "V162" "V163" "V164" "V165" "V166" "V167" "V168" "V169" "V170" "V171" "V172" "V173" "V174" "V175" "V176" "V177" "V178" "V179" "V180" "V181" "V182" "V183" "V184" "V185" "V186" "V187" "V188" "V189" "V190" "V191" "V192" "V193" "V194" "V195" "V196" "V197" "V198" "V199" "V200" "V201" "V202" "V203" "V204" "V205" "V206" "V207" "V208" "V209" "V210" "V211" "V212" "V213" "V214" "V215" "V216" "V217" "V218" "V219" "V220" "V221" "V222" "V223" "V224" "V225" "V226" "V227" "V228" "V229" "V230" "V231" "V232" "V233" "V234" "V235" "V236" "V237" "V238" "V239" "V240" "V241" "V242" "V243" "V244" "V245" "V246" "V247" "V248" "V249" "V250" "V251" "V252" "V253" "V254" "V255" "V256" "V257" "V258" "V259" "V260" "V261" "V262" "V263"
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tests/aliBLAT.fasta deleted 100644 → 0
This source diff could not be displayed because it is too large. You can view the blob instead.
tests/caracTest.dat deleted 100644 → 0
*****************************************
>BLAT:A
size 263 size of the sequence
numAli 43 Number of sequences in alignment
numMulti 43 Number of multiple alignment
partition 498;498;456;446 partition of sequences after PSI-BLAST+filtering
tests/default.conf deleted 100644 → 0
*****************************************
>SequenceRetrieving
method input change this parameter with -r option of JET. See usage of JET to obtain description of this parameter
format fasta fasta: fasta input file, fasta: fasta input file
*****************************************
>QBlast
eValue 1.0E-5 psiblast maximum expected value threshold
results 20000 maximum number of results
url http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi BlastQ server URL
database nr database used
matrix blosum62 matrix used to fetch homologs
gap_existence 11 BLOSUM62=11, PAM30=9, BLOSUM45=15, PAM70=BLOSUM80=10
gap_extension 1 BLOSUM62=1, PAM30=1, BLOSUM45=2, PAM70=BLOSUM80=1
max_iter 3 number of iteration for psi-blast
****************************************
>PDB
url http://www.rcsb.org/pdb/downloadFile.do URL of PDB server
*****************************************
>Filter
min_identity 0.20 min sequence identity
max_identity 0.98 max sequence identity
*****************************************
>Sample
length_cutoff 0.8 minimum sequence length expressed in number of residues
*****************************************
>Software
clustalW /usr/local/bin/clustalw2 clustalW system dependent command
muscle /usr/bin/muscle muscle system dependent command
naccess /home/tekpinar/research/carbone-lab-software/naccess2.1.1/naccess naccess system dependent command
psiblast /usr/bin/psiblast psiblast system dependent command
*****************************************
>Data
substMatrix /home/tekpinar/research/carbone-lab-software/JET2/matrix directory location of matrices used in JET (Blosum62, gonnet and hsdm)
blastDatabases /opt/blastdb directory location of databases used for local blast (nr{0-7})
*****************************************
>ET
coverage 0.95 maximum coverage percentage of trace
freq_cutoff 0.0 minimum frequency of trace residue
msaNumber -1 number of alignments (trees), -1 for JET computting
seqNumber -1 number of sequences in alignments, -1 for JET computting
*****************************************
>Access
probe_radius 1.4 radius of probe used for accessible surface detection
res_cutoff 0.05 minimum percentage accessible surface of a residu
atom_cutoff 0.01 minimum accessible surface of an atom
accessType chain change this parameter with -d option of JET. See usage of JET to obtain description of this parameter
*****************************************
>CV
max_dist 20.0 max distance
*****************************************
>Interface
cutoff 0 minimum percentage accessible surface variation of an interface residu
ligand no (yes|no) keep contact of ligand (SUBSTRATE, PRODUCT and COFACTOR of database ENZYME) to compute interface of protein
enzymeCpd /home/tekpinar/research/carbone-lab-software/JET2/jet/data/enzyme.txt location of file containing database ENZYME
homologousPDB no (yes|no) add interface residues of homologous structures (find in pdb database clustered at 95% of identities) to interface of protein
clusteredPDB /home/tekpinar/research/carbone-lab-software/JET2/jet/data/clusters95.txt location of pdb database clustered at 95% of identities
*****************************************
>Cluster
max_dist 5.0 max distance between atoms to aggregate
analysis 2 change this parameter with -a option of JET. See usage of JET to obtain description of this parameter
namePcCol pc name of the column in results file containing the phisical-chemical score of residues (do not change this parameter)
namePcLCol pcL name of the column in results file containing the residues propensities to be found at prot-lig interfaces (do not change this parameter)
nameTraceCol trace name of the column in results file containing the conservation score of residues (do not change this parameter)
coverage -1 change this parameter with -s option of JET. See usage of JET to obtain description of this parameter
tests/example-gemme-run.sh
#!/bin/bash #!/bin/bash
python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta python $SGEMME_PATH/sgemme.py ../example/aliBLAT.fasta -r input -f ../example/aliBLAT.fasta
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