{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T07:28:01Z","timestamp":1773991681782,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,4,30]],"date-time":"2020-04-30T00:00:00Z","timestamp":1588204800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","award":["175REG"],"award-info":[{"award-number":["175REG"]}],"id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000245","name":"Michael Smith Foundation for Health Research","doi-asserted-by":"publisher","award":["7081"],"award-info":[{"award-number":["7081"]}],"id":[{"id":"10.13039\/501100000245","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\/<\/jats:p>","DOI":"10.1093\/nar\/gkaa288","type":"journal-article","created":{"date-parts":[[2020,4,20]],"date-time":"2020-04-20T11:11:42Z","timestamp":1587381102000},"page":"W154-W161","source":"Crossref","is-referenced-by-count":104,"title":["LIST-S2: taxonomy based sorting of deleterious missense mutations across species"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1317-833X","authenticated-orcid":false,"given":"Nawar","family":"Malhis","sequence":"first","affiliation":[{"name":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}]},{"given":"Matthew","family":"Jacobson","sequence":"first","affiliation":[{"name":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}]},{"given":"Steven J M","family":"Jones","sequence":"first","affiliation":[{"name":"Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada"},{"name":"Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada"}]},{"given":"J\u00f6rg","family":"Gsponer","sequence":"first","affiliation":[{"name":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"},{"name":"Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada"}]}],"member":"286","published-online":{"date-parts":[[2020,4,30]]},"reference":[{"key":"2020062614040960400_B1","doi-asserted-by":"crossref","first-page":"3812","DOI":"10.1093\/nar\/gkg509","article-title":"SIFT: Predicting amino acid changes that affect protein function","volume":"31","author":"Ng","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2020062614040960400_B2","doi-asserted-by":"crossref","first-page":"e46688","DOI":"10.1371\/journal.pone.0046688","article-title":"Predicting the functional effect of amino acid substitutions and indels","volume":"7","author":"Choi","year":"2012","journal-title":"PLoS One"},{"key":"2020062614040960400_B3","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1101\/gr.097857.109","article-title":"Detection of nonneutral substitution rates on mammalian phylogenies","volume":"20","author":"Pollard","year":"2010","journal-title":"Genome Res."},{"key":"2020062614040960400_B4","doi-asserted-by":"crossref","first-page":"e1001025","DOI":"10.1371\/journal.pcbi.1001025","article-title":"Identifying a high fraction of the human genome to be under selective constraint using GERP++","volume":"6","author":"Davydov","year":"2010","journal-title":"PLoS Comput. 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