{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T17:20:31Z","timestamp":1760980831386},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Burst After Duplication with Ancestral Sequence Predictions (BADASP) is a software package for identifying sites that may confer subfamily-specific biological functions in protein families following functional divergence of duplicated proteins. A given protein phylogeny is grouped into subfamilies based on orthology\/paralogy relationships and\/or user definitions. Ancestral sequences are then predicted from the sequence alignment and the functional specificity is calculated using variants of the Burst After Duplication method, which tests for radical amino acid substitutions following gene duplications that are subsequently conserved. Statistics are output along with subfamily groupings and ancestral sequences for an easy analysis with other packages.<\/jats:p>\n               <jats:p>Availability: BADASP is freely available from<\/jats:p>\n               <jats:p>Contact: \u00a0redwards@rcsi.ie<\/jats:p>\n               <jats:p>Supplementary information: A manual with further details can be downloaded from<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti678","type":"journal-article","created":{"date-parts":[[2005,9,14]],"date-time":"2005-09-14T03:13:12Z","timestamp":1126667592000},"page":"4190-4191","source":"Crossref","is-referenced-by-count":17,"title":["BADASP: predicting functional specificity in protein families using ancestral sequences"],"prefix":"10.1093","volume":"21","author":[{"given":"Richard J.","family":"Edwards","sequence":"first","affiliation":[{"name":"Clinical Pharmacology, The Royal College of Surgeons in Ireland \u00a0 123 St Stephen's Green, Dublin 2, Ireland"}]},{"given":"Denis C.","family":"Shields","sequence":"additional","affiliation":[{"name":"Clinical Pharmacology, The Royal College of Surgeons in Ireland \u00a0 123 St Stephen's Green, Dublin 2, Ireland"}]}],"member":"286","published-online":{"date-parts":[[2005,9,13]]},"reference":[{"key":"2023061007210740500_b1","doi-asserted-by":"crossref","first-page":"D197","DOI":"10.1093\/nar\/gki067","article-title":"FunShift: a database of function shift analysis on protein subfamilies","volume":"33","author":"Abhiman","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023061007210740500_b2","first-page":"6","article-title":"Large-scale prediction of function shift in protein families with a focus on enzymatic function","volume":"6","author":"Abhiman","year":"2005","journal-title":"Proteins"},{"key":"2023061007210740500_b3","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1110\/ps.9.4.655","article-title":"A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways","volume":"9","author":"Caffrey","year":"2000","journal-title":"Protein Sci."},{"key":"2023061007210740500_b4","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1016\/S0022-2836(02)01451-1","article-title":"Automatic methods for predicting functionally important residues","volume":"326","author":"del Sol Mesa","year":"2003","journal-title":"J. Mol. Biol."},{"key":"2023061007210740500_b5","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1186\/1471-2105-5-123","article-title":"GASP: Gapped Ancestral Sequence Prediction for proteins","volume":"5","author":"Edwards","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023061007210740500_b6","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1093\/oxfordjournals.molbev.a003824","article-title":"Maximum-likelihood approach for gene family evolution under functional divergence","volume":"18","author":"Gu","year":"2001","journal-title":"Mol. Biol. Evol."},{"key":"2023061007210740500_b7","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1093\/bioinformatics\/18.3.500","article-title":"DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family","volume":"18","author":"Gu","year":"2002","journal-title":"Bioinformatics"},{"key":"2023061007210740500_b8","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1006\/jmbi.2000.4036","article-title":"Analysis and prediction of functional sub-types from protein sequence alignments","volume":"303","author":"Hannenhalli","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2023061007210740500_b9","doi-asserted-by":"crossref","first-page":"3965","DOI":"10.1073\/pnas.050580897","article-title":"Predicting ligand-binding function in families of bacterial receptors","volume":"97","author":"Johnson","year":"2000","journal-title":"Proc. Natl Acad Sci. USA"},{"key":"2023061007210740500_b10","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1110\/ps.03191704","article-title":"Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families","volume":"13","author":"Kalinina","year":"2004","journal-title":"Protein Sci."},{"key":"2023061007210740500_b11","doi-asserted-by":"crossref","first-page":"W424","DOI":"10.1093\/nar\/gkh391","article-title":"SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins","volume":"32","author":"Kalinina","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023061007210740500_b12","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1006\/jmbi.1996.0167","article-title":"An evolutionary trace method defines binding surfaces common to protein families","volume":"257","author":"Lichtarge","year":"1996","journal-title":"J. Mol. Biol."},{"key":"2023061007210740500_b13","first-page":"745","article-title":"Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation","volume":"9","author":"Livingstone","year":"1993","journal-title":"Comput. Appl. Biosci."},{"key":"2023061007210740500_b14","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/S0169-5347(03)00033-8","article-title":"Evolution by gene duplication: an update","volume":"18","author":"Zhang","year":"2003","journal-title":"Trends Ecol. Evol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/22\/4190\/50566262\/bioinformatics_21_22_4190.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/22\/4190\/50566262\/bioinformatics_21_22_4190.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T07:21:17Z","timestamp":1686381677000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/22\/4190\/194819"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,9,13]]},"references-count":14,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2005,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti678","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,11,15]]},"published":{"date-parts":[[2005,9,13]]}}}