{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,31]],"date-time":"2023-10-31T02:21:35Z","timestamp":1698718895226},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Multiple sequence alignment is an important tool to understand and analyze functions of homologous proteins. However, the logic of residue conservation\/variation is usually apparent only in three-dimensional (3D) space, not on a primary sequence level. Thus, in a traditional multiple alignment it is often difficult to directly visualize and analyze key residues because they are masked by other residues along the alignment. Here we present an integrated multiple alignment and 3D structure visualization program that can (1) map and highlight residues from a 1D alignment onto a 3D structure and vice versa and (2) display only the alignment of preselected, key residues. This program, called Visualize Structure Sequence Alignment, also has many other built-in tools that can help analyze multiple sequence alignments.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0liwz@burnham.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl019","type":"journal-article","created":{"date-parts":[[2006,1,25]],"date-time":"2006-01-25T02:48:15Z","timestamp":1138157295000},"page":"887-888","source":"Crossref","is-referenced-by-count":10,"title":["VISSA: a program to visualize structural features from structure sequence alignment"],"prefix":"10.1093","volume":"22","author":[{"given":"Weizhong","family":"Li","sequence":"first","affiliation":[{"name":"Burnham Institute for Medical Research \u00a0 La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"Godzik","sequence":"additional","affiliation":[{"name":"Burnham Institute for Medical Research \u00a0 La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,1,24]]},"reference":[{"key":"2023012409104488200_b1","doi-asserted-by":"crossref","first-page":"3677","DOI":"10.1093\/bioinformatics\/bti602","article-title":"Friend, an integrated analytical front-end application for bioinformatics","volume":"21","author":"Abyzov","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409104488200_b2","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1093\/bioinformatics\/14.4.380","article-title":"MView: a web-compatible database search or multiple alignment viewer","volume":"14","author":"Brown","year":"1998","journal-title":"Bioinformatics"},{"key":"2023012409104488200_b3","doi-asserted-by":"crossref","first-page":"3694","DOI":"10.1093\/bioinformatics\/bth429","article-title":"ViTO: tool for refinement of protein sequence-structure alignments","volume":"20","author":"Catherinot","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012409104488200_b4","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1093\/bioinformatics\/btg430","article-title":"The Jalview Java alignment editor","volume":"20","author":"Clamp","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012409104488200_b5","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409104488200_b6","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1093\/bioinformatics\/btg021","article-title":"Protein family annotation in a multiple alignment viewer","volume":"19","author":"Johnson","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012409104488200_b7","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1093\/bioinformatics\/18.3.452","article-title":"Multiple sequence alignment using partial order graphs","volume":"18","author":"Lee","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012409104488200_b8","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1093\/bioinformatics\/15.3.211","article-title":"DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment","volume":"15","author":"Morgenstern","year":"1999","journal-title":"Bioinformatics"},{"key":"2023012409104488200_b9","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: A novel method for fast and accurate multiple sequence alignment","volume":"302","author":"Notredame","year":"2000","journal-title":"J. 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