{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T09:11:00Z","timestamp":1683969060592},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Here we present the MSA-PAD application, a DNA multiple sequence alignment framework that uses PFAM protein domain information to align DNA sequences encoding either single or multiple protein domains. MSA-PAD has two alignment options: gene and genome mode.<\/jats:p>\n               <jats:p>Availability and Implementation: MSA-PAD is available as a web application (https:\/\/recasgateway.ba.infn.it\/) and as two Taverna workflows corresponding to two alignment modes (Gene mode: http:\/\/www.myexperiment.org\/workflows\/4549.html; Genome Mode: http:\/\/www.myexperiment.org\/workflows\/4551.html).<\/jats:p>\n               <jats:p>Contact: \u00a0g.pesole@ibbe.cnr.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv141","type":"journal-article","created":{"date-parts":[[2015,3,29]],"date-time":"2015-03-29T03:44:55Z","timestamp":1427600695000},"page":"2571-2573","source":"Crossref","is-referenced-by-count":5,"title":["MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information"],"prefix":"10.1093","volume":"31","author":[{"given":"Bachir","family":"Balech","sequence":"first","affiliation":[{"name":"1 Istituto di Biomembrane e Bioenergetica and"}]},{"given":"Saverio","family":"Vicario","sequence":"additional","affiliation":[{"name":"2 Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy,"}]},{"given":"Giacinto","family":"Donvito","sequence":"additional","affiliation":[{"name":"3 Istituto Nazionale di Fisica Nucleare, 70126 Bari, Italy and"}]},{"given":"Alfonso","family":"Monaco","sequence":"additional","affiliation":[{"name":"3 Istituto Nazionale di Fisica Nucleare, 70126 Bari, Italy and"}]},{"given":"Pasquale","family":"Notarangelo","sequence":"additional","affiliation":[{"name":"3 Istituto Nazionale di Fisica Nucleare, 70126 Bari, Italy and"}]},{"given":"Graziano","family":"Pesole","sequence":"additional","affiliation":[{"name":"1 Istituto di Biomembrane e Bioenergetica and"},{"name":"4 Dipartimento Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70126 Bari, Italy"}]}],"member":"286","published-online":{"date-parts":[[2015,3,26]]},"reference":[{"key":"2023051308490103400_btv141-B1","doi-asserted-by":"crossref","first-page":"W7","DOI":"10.1093\/nar\/gkq291","article-title":"TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations","volume":"38","author":"Abascal","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023051308490103400_btv141-B2","doi-asserted-by":"crossref","first-page":"D1168","DOI":"10.1093\/nar\/gkr1144","article-title":"MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa","volume":"40","author":"D'Onorio de Meo","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023051308490103400_btv141-B3","author":"Donvito","year":"2012"},{"key":"2023051308490103400_btv141-B4","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput. Biol."},{"key":"2023051308490103400_btv141-B5","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database","volume":"42","author":"Finn","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023051308490103400_btv141-B6","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","article-title":"EMBOSS: the European Molecular Biology Open Software Suite","volume":"16","author":"Rice","year":"2000","journal-title":"Trends Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/15\/2571\/50306719\/bioinformatics_31_15_2571.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/15\/2571\/50306719\/bioinformatics_31_15_2571.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T08:49:11Z","timestamp":1683967751000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/15\/2571\/187724"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,26]]},"references-count":6,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2015,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv141","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,8,1]]},"published":{"date-parts":[[2015,3,26]]}}}