LIST-S2: taxonomy based sorting of deleterious missense mutations across species

Abstract The separation of deleterious from benign mutations remains a key challenge in the interpretation of genomic data. Computational methods used to sort mutations based on their potential deleteriousness rely largely on conservation measures derived from sequence alignments. Here, we introduce...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Nucleic acids research 2020-07, Vol.48 (W1), p.W154-W161
Hauptverfasser: Malhis, Nawar, Jacobson, Matthew, Jones, Steven J M, Gsponer, Jörg
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page W161
container_issue W1
container_start_page W154
container_title Nucleic acids research
container_volume 48
creator Malhis, Nawar
Jacobson, Matthew
Jones, Steven J M
Gsponer, Jörg
description Abstract The separation of deleterious from benign mutations remains a key challenge in the interpretation of genomic data. Computational methods used to sort mutations based on their potential deleteriousness rely largely on conservation measures derived from sequence alignments. Here, we introduce LIST-S2, a successor to our previously developed approach LIST, which aims to exploit local sequence identity and taxonomy distances in quantifying the conservation of human protein sequences. Unlike its predecessor, LIST-S2 is not limited to human sequences but can assess conservation and make predictions for sequences from any organism. Moreover, we provide a web-tool and downloadable software to compute and visualize the deleteriousness of mutations in user-provided sequences. This web-tool contains an HTML interface and a RESTful API to submit and manage sequences as well as a browsable set of precomputed predictions for a large number of UniProtKB protein sequences of common taxa. LIST-S2 is available at: https://list-s2.msl.ubc.ca/
doi_str_mv 10.1093/nar/gkaa288
format Article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7319545</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/nar/gkaa288</oup_id><sourcerecordid>2396853881</sourcerecordid><originalsourceid>FETCH-LOGICAL-c520t-5fc5711c862040fe7457a3a77f48de3d867daed740dfc68b5e932ba434f0e04f3</originalsourceid><addsrcrecordid>eNp9kc1LwzAYh4Mobk5P3iUnEaQun23qQZDhx2CgsHkOWftmVttmJq24_97q5tCLp_eQhyfv7_0hdEzJBSUpH9bGDxevxjCldlCf8phFIo3ZLuoTTmREiVA9dBDCCyFUUCn2UY8zLpmkcR89TsbTWTRll7gxH6521QrPTYAcB-ebol5gZ3EOJTTgC9cGXBUhQB0AV21jmsLVAZvMuxBwWEJWQDhEe9aUAY42c4Cebm9mo_to8nA3Hl1Pokwy0kTSZjKhNFMxI4JYSIRMDDdJYoXKgecqTnIDeSJIbrNYzSWknM2N4MISIMLyAbpae5ftvII8g7rxptRLX1TGr7Qzhf77UhfPeuHedcJpKoXsBGcbgXdvLYRGd9kyKEtTQ5dUM57GSnKlaIeer9HvpB7s9htK9FcHuutAbzro6JPfm23Zn6N3wOkacO3yX9MnbJ2SRA</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2396853881</pqid></control><display><type>article</type><title>LIST-S2: taxonomy based sorting of deleterious missense mutations across species</title><source>DOAJ Directory of Open Access Journals</source><source>Oxford Journals Open Access Collection</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Malhis, Nawar ; Jacobson, Matthew ; Jones, Steven J M ; Gsponer, Jörg</creator><creatorcontrib>Malhis, Nawar ; Jacobson, Matthew ; Jones, Steven J M ; Gsponer, Jörg</creatorcontrib><description>Abstract The separation of deleterious from benign mutations remains a key challenge in the interpretation of genomic data. Computational methods used to sort mutations based on their potential deleteriousness rely largely on conservation measures derived from sequence alignments. Here, we introduce LIST-S2, a successor to our previously developed approach LIST, which aims to exploit local sequence identity and taxonomy distances in quantifying the conservation of human protein sequences. Unlike its predecessor, LIST-S2 is not limited to human sequences but can assess conservation and make predictions for sequences from any organism. Moreover, we provide a web-tool and downloadable software to compute and visualize the deleteriousness of mutations in user-provided sequences. This web-tool contains an HTML interface and a RESTful API to submit and manage sequences as well as a browsable set of precomputed predictions for a large number of UniProtKB protein sequences of common taxa. LIST-S2 is available at: https://list-s2.msl.ubc.ca/</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkaa288</identifier><identifier>PMID: 32352516</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Web Server Issue</subject><ispartof>Nucleic acids research, 2020-07, Vol.48 (W1), p.W154-W161</ispartof><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c520t-5fc5711c862040fe7457a3a77f48de3d867daed740dfc68b5e932ba434f0e04f3</citedby><cites>FETCH-LOGICAL-c520t-5fc5711c862040fe7457a3a77f48de3d867daed740dfc68b5e932ba434f0e04f3</cites><orcidid>0000-0002-1317-833X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319545/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319545/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32352516$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Malhis, Nawar</creatorcontrib><creatorcontrib>Jacobson, Matthew</creatorcontrib><creatorcontrib>Jones, Steven J M</creatorcontrib><creatorcontrib>Gsponer, Jörg</creatorcontrib><title>LIST-S2: taxonomy based sorting of deleterious missense mutations across species</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract The separation of deleterious from benign mutations remains a key challenge in the interpretation of genomic data. Computational methods used to sort mutations based on their potential deleteriousness rely largely on conservation measures derived from sequence alignments. Here, we introduce LIST-S2, a successor to our previously developed approach LIST, which aims to exploit local sequence identity and taxonomy distances in quantifying the conservation of human protein sequences. Unlike its predecessor, LIST-S2 is not limited to human sequences but can assess conservation and make predictions for sequences from any organism. Moreover, we provide a web-tool and downloadable software to compute and visualize the deleteriousness of mutations in user-provided sequences. This web-tool contains an HTML interface and a RESTful API to submit and manage sequences as well as a browsable set of precomputed predictions for a large number of UniProtKB protein sequences of common taxa. LIST-S2 is available at: https://list-s2.msl.ubc.ca/</description><subject>Web Server Issue</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNp9kc1LwzAYh4Mobk5P3iUnEaQun23qQZDhx2CgsHkOWftmVttmJq24_97q5tCLp_eQhyfv7_0hdEzJBSUpH9bGDxevxjCldlCf8phFIo3ZLuoTTmREiVA9dBDCCyFUUCn2UY8zLpmkcR89TsbTWTRll7gxH6521QrPTYAcB-ebol5gZ3EOJTTgC9cGXBUhQB0AV21jmsLVAZvMuxBwWEJWQDhEe9aUAY42c4Cebm9mo_to8nA3Hl1Pokwy0kTSZjKhNFMxI4JYSIRMDDdJYoXKgecqTnIDeSJIbrNYzSWknM2N4MISIMLyAbpae5ftvII8g7rxptRLX1TGr7Qzhf77UhfPeuHedcJpKoXsBGcbgXdvLYRGd9kyKEtTQ5dUM57GSnKlaIeer9HvpB7s9htK9FcHuutAbzro6JPfm23Zn6N3wOkacO3yX9MnbJ2SRA</recordid><startdate>20200702</startdate><enddate>20200702</enddate><creator>Malhis, Nawar</creator><creator>Jacobson, Matthew</creator><creator>Jones, Steven J M</creator><creator>Gsponer, Jörg</creator><general>Oxford University Press</general><scope>TOX</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-1317-833X</orcidid></search><sort><creationdate>20200702</creationdate><title>LIST-S2: taxonomy based sorting of deleterious missense mutations across species</title><author>Malhis, Nawar ; Jacobson, Matthew ; Jones, Steven J M ; Gsponer, Jörg</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c520t-5fc5711c862040fe7457a3a77f48de3d867daed740dfc68b5e932ba434f0e04f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Web Server Issue</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Malhis, Nawar</creatorcontrib><creatorcontrib>Jacobson, Matthew</creatorcontrib><creatorcontrib>Jones, Steven J M</creatorcontrib><creatorcontrib>Gsponer, Jörg</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Malhis, Nawar</au><au>Jacobson, Matthew</au><au>Jones, Steven J M</au><au>Gsponer, Jörg</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>LIST-S2: taxonomy based sorting of deleterious missense mutations across species</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2020-07-02</date><risdate>2020</risdate><volume>48</volume><issue>W1</issue><spage>W154</spage><epage>W161</epage><pages>W154-W161</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract The separation of deleterious from benign mutations remains a key challenge in the interpretation of genomic data. Computational methods used to sort mutations based on their potential deleteriousness rely largely on conservation measures derived from sequence alignments. Here, we introduce LIST-S2, a successor to our previously developed approach LIST, which aims to exploit local sequence identity and taxonomy distances in quantifying the conservation of human protein sequences. Unlike its predecessor, LIST-S2 is not limited to human sequences but can assess conservation and make predictions for sequences from any organism. Moreover, we provide a web-tool and downloadable software to compute and visualize the deleteriousness of mutations in user-provided sequences. This web-tool contains an HTML interface and a RESTful API to submit and manage sequences as well as a browsable set of precomputed predictions for a large number of UniProtKB protein sequences of common taxa. LIST-S2 is available at: https://list-s2.msl.ubc.ca/</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>32352516</pmid><doi>10.1093/nar/gkaa288</doi><orcidid>https://orcid.org/0000-0002-1317-833X</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0305-1048
ispartof Nucleic acids research, 2020-07, Vol.48 (W1), p.W154-W161
issn 0305-1048
1362-4962
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7319545
source DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry
subjects Web Server Issue
title LIST-S2: taxonomy based sorting of deleterious missense mutations across species
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-08T21%3A11%3A44IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=LIST-S2:%20taxonomy%20based%20sorting%20of%20deleterious%20missense%20mutations%20across%20species&rft.jtitle=Nucleic%20acids%20research&rft.au=Malhis,%20Nawar&rft.date=2020-07-02&rft.volume=48&rft.issue=W1&rft.spage=W154&rft.epage=W161&rft.pages=W154-W161&rft.issn=0305-1048&rft.eissn=1362-4962&rft_id=info:doi/10.1093/nar/gkaa288&rft_dat=%3Cproquest_pubme%3E2396853881%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2396853881&rft_id=info:pmid/32352516&rft_oup_id=10.1093/nar/gkaa288&rfr_iscdi=true