{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T17:13:59Z","timestamp":1764350039183},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2195,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.mrc-lmb.cam.ac.uk\/genomes\/spial\/; supplementary information is available at http:\/\/www.mrc-lmb.cam.ac.uk\/genomes\/spial\/help.html<\/jats:p>\n               <jats:p>Contact: \u00a0ajv@mrc-lmb.cam.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq552","type":"journal-article","created":{"date-parts":[[2010,9,30]],"date-time":"2010-09-30T00:45:30Z","timestamp":1285807530000},"page":"2906-2907","source":"Crossref","is-referenced-by-count":7,"title":["Spial: analysis of subtype-specific features in multiple sequence alignments of proteins"],"prefix":"10.1093","volume":"26","author":[{"given":"Arthur","family":"Wuster","sequence":"first","affiliation":[{"name":"1 Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK and 2Laboratory of Biomolecular research, Paul Scherrer Institut, Villigen CH-5232, Switzerland"}]},{"given":"A. J.","family":"Venkatakrishnan","sequence":"additional","affiliation":[{"name":"1 Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK and 2Laboratory of Biomolecular research, Paul Scherrer Institut, Villigen CH-5232, Switzerland"}]},{"given":"Gebhard F. X.","family":"Schertler","sequence":"additional","affiliation":[{"name":"1 Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK and 2Laboratory of Biomolecular research, Paul Scherrer Institut, Villigen CH-5232, Switzerland"},{"name":"1 Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK and 2Laboratory of Biomolecular research, Paul Scherrer Institut, Villigen CH-5232, Switzerland"}]},{"given":"M. Madan","family":"Babu","sequence":"additional","affiliation":[{"name":"1 Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK and 2Laboratory of Biomolecular research, Paul Scherrer Institut, Villigen CH-5232, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2010,9,29]]},"reference":[{"key":"2023012507553573000_B1","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."},{"key":"2023012507553573000_B2","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":"2023012507553573000_B3","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1016\/j.jmb.2004.08.090","article-title":"Structure of bovine rhodopsin in a trigonal crystal form","volume":"343","author":"Li","year":"2004","journal-title":"J. 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