Please note that the MSA file produced by colabfold (a3m file) can contain gaps in the query sequence. You have to remove them before using it in PRESCOTT. You can remove the gaps with pragrams that have a GUI, such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
Please note that the MSA file produced by colabfold (a3m file) can contain gaps in the query sequence. You have to remove them before using it in PRESCOTT. You can remove the gaps with programs that have a GUI, such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
For testing purpose, you can find some example input files for BLAT protein in data/ folder of this repository.
For testing purpose, you can find some example input files for BLAT protein in data/ folder of this repository.
### Input Data Requirements for prescott
### Input Data Requirements for prescott
...
@@ -76,5 +76,5 @@ PRESCOTT is implemented in Python 3 and R. It has been tested only on Linux. Sin
...
@@ -76,5 +76,5 @@ PRESCOTT is implemented in Python 3 and R. It has been tested only on Linux. Sin
# Cite
# Cite
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
Mustafa Tekpinar, Laurent David, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
<liclass="toctree-l2"><aclass="reference internal"href="#installing-the-dependencies">Installing the dependencies:</a></li>
<liclass="toctree-l2"><aclass="reference internal"href="#installing-the-dependencies">Installing the dependencies:</a></li>
<liclass="toctree-l2"><aclass="reference internal"href="#preparation-of-the-environment-and-installation-of-prescott">Preparation of the environment and installation of PRESCOTT</a></li>
<liclass="toctree-l2"><aclass="reference internal"href="#preparation-of-the-environment-and-installation-of-prescott">Preparation of the environment and installation of PRESCOTT</a></li>
<ahref="input-preparation.html"class="btn btn-neutral float-left"title="Preparing Your Own Input"accesskey="p"rel="prev"><spanclass="fa fa-arrow-circle-left"aria-hidden="true"></span> Previous</a>
<ahref="singularity.html"class="btn btn-neutral float-left"title="Using ESCOTT via Singularity"accesskey="p"rel="prev"><spanclass="fa fa-arrow-circle-left"aria-hidden="true"></span> Previous</a>
<p>Please note that the MSA file produced by colabfold (a3m file) can
<p>Please note that the MSA file produced by colabfold (a3m file) can
contain gaps in the query sequence. You have to remove them before using
contain gaps in the query sequence. You have to remove them before using
it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
it in PRESCOTT. You can remove the gaps with programs that have a GUI,
such as ugene (<aclass="reference external"href="http://ugene.net/">http://ugene.net/</a>) or jalview (<aclass="reference external"href="https://www.jalview.org/">https://www.jalview.org/</a>).</p>
such as ugene (<aclass="reference external"href="http://ugene.net/">http://ugene.net/</a>) or jalview (<aclass="reference external"href="https://www.jalview.org/">https://www.jalview.org/</a>).</p>
<p>For testing purpose, you can find some example input files for BLAT
<p>For testing purpose, you can find some example input files for BLAT
protein in data/ folder of this repository.</p>
protein in data/ folder of this repository.</p>
...
@@ -195,7 +196,7 @@ in the docs folder of this repository):</p>
...
@@ -195,7 +196,7 @@ in the docs folder of this repository):</p>
</section>
</section>
<sectionid="citation">
<sectionid="citation">
<h2>Citation<aclass="headerlink"href="#citation"title="Permalink to this heading"></a></h2>
<h2>Citation<aclass="headerlink"href="#citation"title="Permalink to this heading"></a></h2>
<p>Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.</p>
<p>Mustafa Tekpinar, Laurent David, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.</p>
Search.setIndex({"docnames":["analysis","docker","index","input-preparation","installation","introduction","singularity"],"filenames":["analysis.rst","docker.rst","index.rst","input-preparation.rst","installation.rst","introduction.rst","singularity.rst"],"titles":["Analyzing and Modifying the ESCOTT Output","Using ESCOTT via Docker","Welcome to PRESCOTT documentation!","Preparing Your Own Input","Installation","Introduction","Using ESCOTT via Singularity"],"terms":{"There":[0,3],"hardcod":0,"limit":0,"howev":[0,1,3,5,6],"valu":0,"rang":0,"between":0,"12":0,"2":[0,5,6],"gener":0,"The":[0,1,3,5],"lower":0,"mean":0,"impact":[0,1,3],"while":0,"close":0,"0":[0,1,3,4,5,6],"doe":[0,3],"have":[0,1,3,4,5,6],"ani":[0,5],"signific":0,"we":[0,1,3,4,5],"should":[0,4,5],"note":[0,1,4,5,6],"most":[0,5],"ar":[0,1,3,4,5,6],"deleteri":0,"alwai":0,"case":[0,1,4],"By":[0,5],"default":[0,2,5],"onli":[0,1,4,5],"combin":[0,5],"independ":0,"epistat":[0,5],"three":[0,5],"file":[0,1,2,3,5,6],"myprot_normpred_evolcombi":0,"txt":[0,1,5],"myprot":0,"short":0,"name":[0,1],"msa":[0,1,2,4,5],"your":[0,1,2,4,5,6],"protein":[0,1,3,5],"contain":[0,1,3,4,5],"20":[0,4],"row":0,"amino":0,"acid":0,"alphabet":0,"order":[0,1,5],"l":[0,3],"column":[0,3],"where":[0,3,6],"number":0,"interest":[0,1,3],"sinc":[0,4,5],"thi":[0,1,3,4,5,6],"horizont":0,"easi":0,"read":0,"r":[0,4,5],"python":[0,4,5],"difficult":0,"find":[0,5,6],"you":[0,1,3,4,5,6],"myprot_normpred_evolcombitranspos":[],"As":[0,1],"impli":0,"transpos":0,"version":[0,4,5,6],"result":0,"It":[0,1,3,4,5],"easier":0,"just":[],"check":[1,4],"correspond":[],"prepar":[1,2,6],"imag":[0,3,4,5,6],"oranges_r":[],"matplotlib":0,"color":0,"map":0,"can":[0,1,3,4,5,6],"chang":[0,1,3,6],"ad":[0,3,4],"colormap":0,"turbo_r":0,"more":[0,1,3],"fanci":0,"look":0,"dure":0,"call":[0,1,4,5],"argument":0,"accept":0,"all":[0,1,3,4,5],"If":[0,1,4,5,6],"want":[0,1,3,6],"see":[0,1,3],"contribut":0,"well":[0,1],"add":[0,4],"verbos":0,"true":[0,4],"us":[0,2,3,4,5],"predict":[0,5],"same":[0,1],"format":[0,1,3,5],"a2c":0,"6":[0,6],"23":0,"a2d":0,"1":[0,3,5,6],"d286f":0,"need":[1,5,6],"instal":[1,2,6],"machin":1,"consult":[1,5],"follow":[1,3,4,5,6],"page":[1,2,6],"http":[1,3,4,5,6],"doc":[1,5],"com":[1,3,4,5,6],"i":[1,3,4,6],"am":1,"assum":[0,1,5],"some":[1,5],"basic":[1,5],"familiar":1,"linux":[1,4,5],"unix":1,"maco":1,"termin":[1,3,5],"command":[1,3,4,5],"let":[1,3,5],"s":[1,3,4,5],"start":[1,3],"our":[1,3,4,5],"favorit":1,"app":1,"must":[1,5,6],"creat":[1,3],"folder":[1,3,4,5,6],"tutori":1,"go":[1,3,4,6],"empti":1,"mkdir":[1,4],"cd":[1,3,4],"download":[1,4,5],"sampl":1,"provid":[1,6],"repositori":[1,4,5,6],"exercis":1,"first":[1,5,6],"sequenc":[0,1,3,5],"align":[1,3,5],"fasta":[0,1,3,5,6],"wget":[1,4],"gitlab":[1,4],"lcqb":[1,4],"upmc":[1,4],"fr":[1,4],"tekpinar":[1,3,4,5,6],"raw":[1,2],"8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936":1,"aliblat":[1,6],"don":1,"t":1,"try":1,"curl":1,"pleas":[1,3,4,5,6],"verifi":1,"now":[1,3,4],"pdb":[1,2,5,6],"databank":1,"blat":[1,5,6],"af2":[1,6],"In":[1,4,5,6],"make":[1,3,4],"sure":[1,3],"sudo":[1,3,4,6],"h":[1,6],"show":[1,5,6],"list":[1,3,4],"option":[1,5],"good":1,"track":1,"On":[1,5],"mai":[0,1],"word":1,"befor":[1,3,5],"ti":[1,3],"rm":[1,3,4],"mount":[1,3],"type":[1,3,5],"bind":[1,3],"sourc":[1,3,4,5,6],"pwd":[1,3,6],"target":[1,3],"home":[1,3,4,6],"research":[1,3,4,5],"myexampl":[1,3],"v1":[1,3,6],"3":[4,5,6],"virtual":1,"oper":1,"system":[1,4,6],"previou":1,"when":1,"ls":[1,3],"suppos":[1,3],"host":1,"place":1,"step":[1,3,4,5,6],"evolutionari":[1,4,5],"inform":[1,5],"from":[1,3,4,5,6],"an":[0,1,3,4,6],"esgemme_path":[],"py":[],"f":4,"after":[0,1,4],"few":[1,3],"minut":[1,3],"least":1,"two":[1,5,6],"blat_normpred_evolcombi":1,"png":[0,1,5],"util":[1,4],"structur":[1,3,5],"highli":[1,5],"recommend":[1,4,5],"pdbfile":[1,5,6],"normweightmod":[],"sstjetormax":[],"bunch":1,"mut":1,"simpl":1,"text":1,"each":[0,1,5],"line":[1,4,5],"d26a":1,"fortun":1,"master":[1,4],"stiffler_2015_blat_ecolx":1,"similar":1,"possibl":[1,5],"wai":[1,5],"do":[1,3,4],"without":1,"m":[1,5],"includ":1,"code":[],"bash":[1,5],"output":[1,2,5],"complet":1,"differ":[1,6],"scan":1,"its":[1,4,5],"separ":[1,5],"space":1,"addit":[1,5,6],"won":1,"like":[0,1,3,4,5],"sometim":1,"doubl":1,"tripl":1,"perform":[1,6],"e26d":1,"y44r":1,"e56n":1,"a77f":1,"h94v":1,"second":1,"colon":[1,5],"charact":[0,1],"via":[2,5],"docker":[2,3,4,5,6],"requir":[2,3,4],"get":[2,4],"exampl":[2,3,5],"input":2,"data":[2,6],"singl":[2,5],"point":[2,5],"mutat":[2,3,5],"calcul":[2,5],"multipl":[2,3,5],"run":[2,3,6],"sever":2,"job":2,"analyz":2,"modifi":[2,4],"score":[2,5],"Their":2,"interpret":2,"entir":[2,5],"landscap":[2,5],"select":[2,3],"own":[2,4],"colabfold":[2,5],"depend":[2,3,5],"environ":2,"configur":2,"conf":2,"index":2,"modul":[2,5],"search":2,"understand":3,"certain":3,"gap":[3,5],"quickest":3,"method":3,"obtain":[3,4,5],"both":[3,5,6],"web":[3,4,5],"site":[3,4,5],"colab":[3,5],"googl":[3,5],"github":[3,4,5,6],"sokrypton":[3,5],"blob":[3,5,6],"main":[3,5,6],"alphafold2":[3,5],"ipynb":[3,5],"sign":3,"gmail":3,"account":[3,4],"click":3,"connect":3,"button":3,"top":3,"right":3,"hand":[3,5],"side":3,"clean":[3,4],"query_sequ":3,"box":3,"past":3,"For":[3,5],"me":3,"adenyl":3,"kinas":3,"ak":3,"my":[3,4],"www":[3,4,5],"rcsb":3,"org":[3,4,5],"entri":3,"4ake":3,"displai":3,"jobnam":3,"someth":3,"sens":3,"menu":3,"bar":3,"notebook":3,"edit":3,"view":3,"insert":3,"runtim":3,"tool":3,"help":[3,5],"process":3,"take":3,"hour":3,"size":3,"give":3,"a3m":[3,5],"up":[3,5],"5":[1,3],"model":[3,5],"put":3,"directori":[3,5],"unfortun":3,"those":3,"gui":[3,5],"program":[0,3,4],"ugen":[3,5],"jalview":[3,5],"labor":3,"intens":3,"procedur":3,"here":[3,4,6],"small":3,"develop":[3,4],"esgemm":4,"script":[1,3,4,5],"hhsuit":[3,4],"convert":3,"reformat":3,"pl":3,"fa":3,"final":[3,5],"demust":3,"removegap":3,"o":[3,4],"ake_nogap":3,"congratul":3,"ii":[],"myprotein":3,"implement":[4,5],"ha":[0,4,5],"been":[4,5],"test":[4,5],"mani":[4,5,6],"determin":[4,5],"user":[4,5],"come":[4,5],"extern":4,"joint":4,"tree":4,"jet2":4,"java":4,"naccess":4,"bioinf":4,"manchest":4,"ac":4,"uk":4,"muscl":4,"drive5":[],"seqinr":4,"packag":[4,5],"cran":4,"project":4,"html":[],"dssp":4,"secondari":4,"These":6,"abl":4,"defin":4,"export":4,"variabl":4,"path":[1,4],"insid":[1,4],"import":[1,4,5],"essenti":4,"paramet":[4,5],"part":[3,4],"intern":4,"etc":[4,6],"correct":4,"softwar":4,"section":4,"accord":[4,5],"ubuntu":4,"22":4,"04":4,"apt":4,"updat":[4,6],"fix":4,"miss":4,"y":4,"properti":4,"common":4,"autotool":4,"dev":4,"automak":4,"build":[4,6],"python3":4,"pip":4,"base":[4,5],"core":4,"jre":4,"ncbi":4,"blast":4,"nano":4,"less":4,"csh":4,"hmmer":4,"libboost":4,"rf":4,"var":4,"lib":4,"tmp":4,"otherwis":4,"work":4,"properli":4,"cmbi":4,"archiv":4,"ref":4,"head":4,"zip":4,"unzip":4,"autogen":4,"sh":4,"ln":4,"usr":4,"local":[1,4],"bin":4,"mkdssp":4,"soedinglab":4,"hh":4,"suit":4,"releas":[4,6],"v3":4,"avx2":4,"tar":4,"gz":4,"mv":4,"xvfz":4,"perman":4,"bashrc":4,"profil":4,"bash_profil":4,"locat":[4,6],"wa":4,"therefor":[4,5],"Then":[1,4],"rscript":4,"e":[4,5],"repo":4,"ev_coupl":4,"pip3":4,"debbiemarkslab":4,"plmc":4,"openmp32":4,"cp":4,"one":[0,3],"last":3,"reach":3,"goal":3,"id":3,"descript":3,"too":3,"long":3,"shorten":3,"them":[3,5,6],"awk":3,"begin":3,"fs":3,"nf":3,"printf":3,"n":3,"els":3,"print":3,"ake_nogaps_short_nam":3,"recheck":3,"remov":[3,5],"extra":3,"jet2_path":4,"open":[0,4],"gedit":4,"below":[4,5],"end":[4,5],"save":4,"exit":4,"forget":4,"replac":4,"so":4,"taken":4,"Of":4,"cours":4,"would":[4,5],"git":4,"clone":4,"b":4,"4":6,"prescott":[1,3,6],"escott":2,"popul":5,"awar":5,"effect":[0,5],"introduct":2,"usag":2,"cite":[],"licens":[],"mit":[],"logo":[],"made":5,"other":5,"incorpor":5,"frequenc":5,"due":[5,6],"mandatori":5,"queri":[0,5],"One":5,"fastest":5,"produc":[0,5],"pragram":5,"net":5,"purpos":5,"normpredcombi":5,"gnomad":5,"csv":[0,5],"broadinstitut":5,"document":5,"further":5,"detail":5,"inputali":5,"issu":5,"A":5,"quick":5,"access":5,"posit":5,"altern":5,"set":5,"given":5,"g":5,"d136r":5,"v271a":5,"mlh1_normpred_evolcombi":5,"gnomad_v2":5,"1_mlh1_human_ensg00000076242":5,"mlh1":5,"which":5,"frequeci":[],"link":5,"soon":[],"img":[],"shield":[],"io":[],"badg":[],"yellow":[],"svg":[],"opensourc":[],"what":2,"citat":2,"mustafa":5,"thoma":5,"henri":5,"alessandra":5,"carbon":5,"accur":5,"missens":5,"myprot_normpred_evolcombitransposedranksort":0,"revers":0,"ranksort":0,"spreadsheet":0,"ms":0,"excel":0,"origin":0,"indic":0,"high":[0,6],"longer":0,"than":0,"500":0,"residu":0,"segment":0,"autom":1,"within":1,"v":1,"veri":1,"execut":1,"typic":1,"abov":1,"gnomad_v4":5,"0_mlh1_human_ensg00000076242":5,"v4":5,"comprehens":5,"publicli":5,"avail":5,"human":5,"dataset":5,"far":5,"know":5,"v2":5,"specifi":5,"gnomadvers":5,"about":5,"non":5,"variant":5,"pathogen":5,"benign":5,"label":5,"clinvar":5,"vs":5,"how":[5,6],"affect":5,"acalcul":5,"comput":6,"permiss":6,"reason":6,"singulartii":6,"sif":6,"onlin":6,"thing":6,"instruct":6,"sylab":6,"md":6,"deb":6,"rpm":6,"exec":6,"your_singularity_dir":6,"singular":2},"objects":{},"objtypes":{},"objnames":{},"titleterms":{"analyz":0,"modifi":0,"esgemm":[],"output":0,"raw":0,"score":0,"Their":0,"interpret":0,"entir":[0,1],"singl":[0,1],"point":[0,1],"mutat":[0,1],"landscap":[0,1],"calcul":[0,1],"select":0,"multipl":[0,1],"us":[1,6],"via":[1,6],"docker":1,"requir":[1,5],"get":1,"exampl":1,"input":[1,3,5],"data":[1,5],"obtain":1,"predict":1,"effect":1,"subset":1,"run":[1,5],"sever":1,"job":1,"welcom":2,"s":[],"document":2,"content":2,"indic":2,"tabl":2,"prepar":[3,4],"your":3,"own":3,"msa":3,"pdb":3,"colabfold":3,"instal":[4,5],"depend":4,"sourc":[],"code":[],"environ":4,"configur":4,"default":4,"conf":4,"file":4,"prescott":[2,4,5],"escott":[0,1,5,6],"popul":[],"awar":[],"epistat":[],"structur":[],"model":[],"introduct":5,"usag":5,"program":5,"cite":[],"what":5,"citat":5,"singular":6},"envversion":{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":6,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx":56}})
Search.setIndex({"docnames":["analysis","docker","index","input-preparation","installation","introduction","singularity"],"filenames":["analysis.rst","docker.rst","index.rst","input-preparation.rst","installation.rst","introduction.rst","singularity.rst"],"titles":["Analyzing and Modifying the ESCOTT Output","Using ESCOTT via Docker","Welcome to PRESCOTT documentation!","Preparing Your Own Input","Installation","Introduction","Using ESCOTT via Singularity"],"terms":{"There":[0,3],"hardcod":0,"limit":0,"howev":[0,1,3,5,6],"valu":0,"rang":0,"between":0,"12":0,"2":[0,5,6],"gener":0,"The":[0,1,3,5],"lower":0,"mean":0,"impact":[0,1,3],"while":0,"close":0,"0":[0,1,3,4,5,6],"doe":[0,3],"have":[0,1,3,4,5,6],"ani":[0,5],"signific":0,"we":[0,1,3,4,5],"should":[0,4,5],"note":[0,1,4,5,6],"most":[0,5],"ar":[0,1,3,4,5,6],"deleteri":0,"alwai":0,"case":[0,1,4],"By":[0,5],"default":[0,2,5],"onli":[0,1,4,5],"combin":[0,5],"independ":0,"epistat":[0,5],"three":[0,5],"file":[0,1,2,3,5,6],"myprot_normpred_evolcombi":0,"txt":[0,1,5],"myprot":0,"short":0,"name":[0,1],"msa":[0,1,2,4,5],"your":[0,1,2,4,5,6],"protein":[0,1,3,5],"contain":[0,1,3,4,5],"20":[0,4],"row":0,"amino":0,"acid":0,"alphabet":0,"order":[0,1,5],"l":[0,3],"column":[0,3],"where":[0,3,6],"number":0,"interest":[0,1,3],"sinc":[0,4,5],"thi":[0,1,3,4,5,6],"horizont":0,"easi":0,"read":0,"r":[0,4,5],"python":[0,4,5],"difficult":0,"find":[0,5,6],"you":[0,1,3,4,5,6],"myprot_normpred_evolcombitranspos":[],"As":[0,1],"impli":0,"transpos":0,"version":[0,4,5,6],"result":0,"It":[0,1,3,4,5],"easier":0,"just":[],"check":[1,4],"correspond":[],"prepar":[1,2,6],"imag":[0,3,4,5,6],"oranges_r":[],"matplotlib":0,"color":0,"map":0,"can":[0,1,3,4,5,6],"chang":[0,1,3,6],"ad":[0,3,4],"colormap":0,"turbo_r":0,"more":[0,1,3],"fanci":0,"look":0,"dure":0,"call":[0,1,4,5],"argument":0,"accept":0,"all":[0,1,3,4,5],"If":[0,1,4,5,6],"want":[0,1,3,6],"see":[0,1,3],"contribut":0,"well":[0,1],"add":[0,4],"verbos":0,"true":[0,4],"us":[0,2,3,4,5],"predict":[0,5],"same":[0,1],"format":[0,1,3,5],"a2c":0,"6":[0,6],"23":0,"a2d":0,"1":[0,3,5,6],"d286f":0,"need":[1,5,6],"instal":[1,2,6],"machin":1,"consult":[1,5],"follow":[1,3,4,5,6],"page":[1,2,6],"http":[1,3,4,5,6],"doc":[1,5],"com":[1,3,4,5,6],"i":[1,3,4,6],"am":1,"assum":[0,1,5],"some":[1,5],"basic":[1,5],"familiar":1,"linux":[1,4,5],"unix":1,"maco":1,"termin":[1,3,5],"command":[1,3,4,5],"let":[1,3,5],"s":[1,3,4,5],"start":[1,3],"our":[1,3,4,5],"favorit":1,"app":1,"must":[1,5,6],"creat":[1,3],"folder":[1,3,4,5,6],"tutori":1,"go":[1,3,4,6],"empti":1,"mkdir":[1,4],"cd":[1,3,4],"download":[1,4,5],"sampl":1,"provid":[1,6],"repositori":[1,4,5,6],"exercis":1,"first":[1,5,6],"sequenc":[0,1,3,5],"align":[1,3,5],"fasta":[0,1,3,5,6],"wget":[1,4],"gitlab":[1,4],"lcqb":[1,4],"upmc":[1,4],"fr":[1,4],"tekpinar":[1,3,4,5,6],"raw":[1,2],"8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936":1,"aliblat":[1,6],"don":1,"t":1,"try":1,"curl":1,"pleas":[1,3,4,5,6],"verifi":1,"now":[1,3,4],"pdb":[1,2,5,6],"databank":1,"blat":[1,5,6],"af2":[1,6],"In":[1,4,5,6],"make":[1,3,4],"sure":[1,3],"sudo":[1,3,4,6],"h":[1,6],"show":[1,5,6],"list":[1,3,4],"option":[1,5],"good":1,"track":1,"On":[1,5],"mai":[0,1],"word":1,"befor":[1,3,5],"ti":[1,3],"rm":[1,3,4],"mount":[1,3],"type":[1,3,5],"bind":[1,3],"sourc":[1,3,4,5,6],"pwd":[1,3,6],"target":[1,3],"home":[1,3,4,6],"research":[1,3,4,5],"myexampl":[1,3],"v1":[1,3,6],"3":[4,5,6],"virtual":1,"oper":1,"system":[1,4,6],"previou":1,"when":1,"ls":[1,3],"suppos":[1,3],"host":1,"place":1,"step":[1,3,4,5,6],"evolutionari":[1,4,5],"inform":[1,5],"from":[1,3,4,5,6],"an":[0,1,3,4,6],"esgemme_path":[],"py":[],"f":4,"after":[0,1,4],"few":[1,3],"minut":[1,3],"least":1,"two":[1,5,6],"blat_normpred_evolcombi":1,"png":[0,1,5],"util":[1,4],"structur":[1,3,5],"highli":[1,5],"recommend":[1,4,5],"pdbfile":[1,5,6],"normweightmod":[],"sstjetormax":[],"bunch":1,"mut":1,"simpl":1,"text":1,"each":[0,1,5],"line":[1,4,5],"d26a":1,"fortun":1,"master":[1,4],"stiffler_2015_blat_ecolx":1,"similar":1,"possibl":[1,5],"wai":[1,5],"do":[1,3,4],"without":1,"m":[1,5],"includ":1,"code":[],"bash":[1,5],"output":[1,2,5],"complet":1,"differ":[1,6],"scan":1,"its":[1,4,5],"separ":[1,5],"space":1,"addit":[1,5,6],"won":1,"like":[0,1,3,4,5],"sometim":1,"doubl":1,"tripl":1,"perform":[1,6],"e26d":1,"y44r":1,"e56n":1,"a77f":1,"h94v":1,"second":1,"colon":[1,5],"charact":[0,1],"via":[2,5],"docker":[2,3,4,5,6],"requir":[2,3,4],"get":[2,4],"exampl":[2,3,5],"input":2,"data":[2,6],"singl":[2,5],"point":[2,5],"mutat":[2,3,5],"calcul":[2,5],"multipl":[2,3,5],"run":[2,3,6],"sever":2,"job":2,"analyz":2,"modifi":[2,4],"score":[2,5],"Their":2,"interpret":2,"entir":[2,5],"landscap":[2,5],"select":[2,3],"own":[2,4],"colabfold":[2,5],"depend":[2,3,5],"environ":2,"configur":2,"conf":2,"index":2,"modul":[2,5],"search":2,"understand":3,"certain":3,"gap":[3,5],"quickest":3,"method":3,"obtain":[3,4,5],"both":[3,5,6],"web":[3,4,5],"site":[3,4,5],"colab":[3,5],"googl":[3,5],"github":[3,4,5,6],"sokrypton":[3,5],"blob":[3,5,6],"main":[3,5,6],"alphafold2":[3,5],"ipynb":[3,5],"sign":3,"gmail":3,"account":[3,4],"click":3,"connect":3,"button":3,"top":3,"right":3,"hand":[3,5],"side":3,"clean":[3,4],"query_sequ":3,"box":3,"past":3,"For":[3,5],"me":3,"adenyl":3,"kinas":3,"ak":3,"my":[3,4],"www":[3,4,5],"rcsb":3,"org":[3,4,5],"entri":3,"4ake":3,"displai":3,"jobnam":3,"someth":3,"sens":3,"menu":3,"bar":3,"notebook":3,"edit":3,"view":3,"insert":3,"runtim":3,"tool":3,"help":[3,5],"process":3,"take":3,"hour":3,"size":3,"give":3,"a3m":[3,5],"up":[3,5],"5":[1,3],"model":[3,5],"put":3,"directori":[3,5],"unfortun":3,"those":3,"gui":[3,5],"program":[0,3,4],"ugen":[3,5],"jalview":[3,5],"labor":3,"intens":3,"procedur":3,"here":[3,4,6],"small":3,"develop":[3,4],"esgemm":4,"script":[1,3,4,5],"hhsuit":[3,4],"convert":3,"reformat":3,"pl":3,"fa":3,"final":[3,5],"demust":3,"removegap":3,"o":[3,4],"ake_nogap":3,"congratul":3,"ii":[],"myprotein":3,"implement":[4,5],"ha":[0,4,5],"been":[4,5],"test":[4,5],"mani":[4,5,6],"determin":[4,5],"user":[4,5],"come":[4,5],"extern":4,"joint":4,"tree":4,"jet2":4,"java":4,"naccess":4,"bioinf":4,"manchest":4,"ac":4,"uk":4,"muscl":4,"drive5":[],"seqinr":4,"packag":[4,5],"cran":4,"project":4,"html":[],"dssp":4,"secondari":4,"These":6,"abl":4,"defin":4,"export":4,"variabl":4,"path":[1,4],"insid":[1,4],"import":[1,4,5],"essenti":4,"paramet":[4,5],"part":[3,4],"intern":4,"etc":[4,6],"correct":4,"softwar":4,"section":4,"accord":[4,5],"ubuntu":4,"22":4,"04":4,"apt":4,"updat":[4,6],"fix":4,"miss":4,"y":4,"properti":4,"common":4,"autotool":4,"dev":4,"automak":4,"build":[4,6],"python3":4,"pip":4,"base":[4,5],"core":4,"jre":4,"ncbi":4,"blast":4,"nano":4,"less":4,"csh":4,"hmmer":4,"libboost":4,"rf":4,"var":4,"lib":4,"tmp":4,"otherwis":4,"work":4,"properli":4,"cmbi":4,"archiv":4,"ref":4,"head":4,"zip":4,"unzip":4,"autogen":4,"sh":4,"ln":4,"usr":4,"local":[1,4],"bin":4,"mkdssp":4,"soedinglab":4,"hh":4,"suit":4,"releas":[4,6],"v3":4,"avx2":4,"tar":4,"gz":4,"mv":4,"xvfz":4,"perman":4,"bashrc":4,"profil":4,"bash_profil":4,"locat":[4,6],"wa":4,"therefor":[4,5],"Then":[1,4],"rscript":4,"e":[4,5],"repo":4,"ev_coupl":4,"pip3":4,"debbiemarkslab":4,"plmc":4,"openmp32":4,"cp":4,"one":[0,3],"last":3,"reach":3,"goal":3,"id":3,"descript":3,"too":3,"long":3,"shorten":3,"them":[3,5,6],"awk":3,"begin":3,"fs":3,"nf":3,"printf":3,"n":3,"els":3,"print":3,"ake_nogaps_short_nam":3,"recheck":3,"remov":[3,5],"extra":3,"jet2_path":4,"open":[0,4],"gedit":4,"below":[4,5],"end":[4,5],"save":4,"exit":4,"forget":4,"replac":4,"so":4,"taken":4,"Of":4,"cours":4,"would":[4,5],"git":4,"clone":4,"b":4,"4":6,"prescott":[1,3,6],"escott":2,"popul":5,"awar":5,"effect":[0,5],"introduct":2,"usag":2,"cite":[],"licens":[],"mit":[],"logo":[],"made":5,"other":5,"incorpor":5,"frequenc":5,"due":[5,6],"mandatori":5,"queri":[0,5],"One":5,"fastest":5,"produc":[0,5],"pragram":[],"net":5,"purpos":5,"normpredcombi":5,"gnomad":5,"csv":[0,5],"broadinstitut":5,"document":5,"further":5,"detail":5,"inputali":5,"issu":5,"A":5,"quick":5,"access":5,"posit":5,"altern":5,"set":5,"given":5,"g":5,"d136r":5,"v271a":5,"mlh1_normpred_evolcombi":5,"gnomad_v2":5,"1_mlh1_human_ensg00000076242":5,"mlh1":5,"which":5,"frequeci":[],"link":5,"soon":[],"img":[],"shield":[],"io":[],"badg":[],"yellow":[],"svg":[],"opensourc":[],"what":2,"citat":2,"mustafa":5,"thoma":5,"henri":5,"alessandra":5,"carbon":5,"accur":5,"missens":5,"myprot_normpred_evolcombitransposedranksort":0,"revers":0,"ranksort":0,"spreadsheet":0,"ms":0,"excel":0,"origin":0,"indic":0,"high":[0,6],"longer":0,"than":0,"500":0,"residu":0,"segment":0,"autom":1,"within":1,"v":1,"veri":1,"execut":1,"typic":1,"abov":1,"gnomad_v4":5,"0_mlh1_human_ensg00000076242":5,"v4":5,"comprehens":5,"publicli":5,"avail":5,"human":5,"dataset":5,"far":5,"know":5,"v2":5,"specifi":5,"gnomadvers":5,"about":5,"non":5,"variant":5,"pathogen":5,"benign":5,"label":5,"clinvar":5,"vs":5,"how":[5,6],"affect":5,"acalcul":5,"comput":6,"permiss":6,"reason":6,"singulartii":6,"sif":6,"onlin":6,"thing":6,"instruct":6,"sylab":6,"md":6,"deb":6,"rpm":6,"exec":6,"your_singularity_dir":6,"singular":2,"laurent":5,"david":5},"objects":{},"objtypes":{},"objnames":{},"titleterms":{"analyz":0,"modifi":0,"esgemm":[],"output":0,"raw":0,"score":0,"Their":0,"interpret":0,"entir":[0,1],"singl":[0,1],"point":[0,1],"mutat":[0,1],"landscap":[0,1],"calcul":[0,1],"select":0,"multipl":[0,1],"us":[1,6],"via":[1,6],"docker":1,"requir":[1,5],"get":1,"exampl":1,"input":[1,3,5],"data":[1,5],"obtain":1,"predict":1,"effect":1,"subset":1,"run":[1,5],"sever":1,"job":1,"welcom":2,"s":[],"document":2,"content":2,"indic":2,"tabl":2,"prepar":[3,4],"your":3,"own":3,"msa":3,"pdb":3,"colabfold":3,"instal":[4,5],"depend":4,"sourc":[],"code":[],"environ":4,"configur":4,"default":4,"conf":4,"file":4,"prescott":[2,4,5],"escott":[0,1,5,6],"popul":[],"awar":[],"epistat":[],"structur":[],"model":[],"introduct":5,"usag":5,"program":5,"cite":[],"what":5,"citat":5,"singular":6},"envversion":{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":6,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx":56}})
Please note that the MSA file produced by colabfold (a3m file) can
Please note that the MSA file produced by colabfold (a3m file) can
contain gaps in the query sequence. You have to remove them before using
contain gaps in the query sequence. You have to remove them before using
it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
it in PRESCOTT. You can remove the gaps with programs that have a GUI,
such as ugene (\sphinxurl{http://ugene.net/}) or jalview (\sphinxurl{https://www.jalview.org/}).
such as ugene (\sphinxurl{http://ugene.net/}) or jalview (\sphinxurl{https://www.jalview.org/}).
\sphinxAtStartPar
\sphinxAtStartPar
...
@@ -256,7 +256,7 @@ in the docs folder of this repository):
...
@@ -256,7 +256,7 @@ in the docs folder of this repository):
\section{Citation}
\section{Citation}
\label{\detokenize{introduction:citation}}
\label{\detokenize{introduction:citation}}
\sphinxAtStartPar
\sphinxAtStartPar
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
Mustafa Tekpinar, Laurent David, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
Please note that the MSA file produced by colabfold (a3m file) can
Please note that the MSA file produced by colabfold (a3m file) can
contain gaps in the query sequence. You have to remove them before using
contain gaps in the query sequence. You have to remove them before using
it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
it in PRESCOTT. You can remove the gaps with programs that have a GUI,
such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
For testing purpose, you can find some example input files for BLAT
For testing purpose, you can find some example input files for BLAT
...
@@ -129,7 +129,7 @@ in the docs folder of this repository):
...
@@ -129,7 +129,7 @@ in the docs folder of this repository):
Citation
Citation
--------
--------
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
Mustafa Tekpinar, Laurent David, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
