{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T10:51:34Z","timestamp":1762339894579,"version":"3.30.2"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: \u00a0BlastAlign uses NCBI blastn to build a multiple nucleotide alignment and is intended for use with sequences that have large indels or are otherwise difficult to align globally. The program builds a matrix representing regions of homology along the sequences, from which it selects the \u2018most representative\u2019 sequence and then extracts the blastn query-anchored multiple alignment for this sequence. The matrix is printed and allows subgroups to be identified visually and an option allows other sequences to be used as the \u2018most representative\u2019. The program contains elements of both Perl and Python and will run on UNIX (including Mac OSX) and DOS. An additional Perl program BlastAlignP uses tblastn to align nucleotide sequences to a single amino acid sequence, thus allowing an open reading frame to be maintained in the resulting multiple alignment.<\/jats:p><jats:p>Availability: It is freely available at http:\/\/www.bio.ic.ac.uk\/research\/belshaw\/BlastAlign.tar and at http:\/\/evolve.zoo.ox.ac.uk\/software\/blastalign<\/jats:p><jats:p>Contact: \u00a0r.belshaw@imperial.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth459","type":"journal-article","created":{"date-parts":[[2004,8,14]],"date-time":"2004-08-14T01:32:45Z","timestamp":1092447165000},"page":"122-123","source":"Crossref","is-referenced-by-count":51,"title":["<i>BlastAlign<\/i>: a program that uses<i>blast<\/i>to align problematic nucleotide sequences"],"prefix":"10.1093","volume":"21","author":[{"given":"Robert","family":"Belshaw","sequence":"first","affiliation":[]},{"given":"Aris","family":"Katzourakis","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,8,13]]},"reference":[{"key":"2023013107190278100_B1","doi-asserted-by":"crossref","unstructured":"Bray, N., Dubchak, I., Pachter, L. 2003AVID: a global alignment program. Genome Res.1397\u2013102","DOI":"10.1101\/gr.789803"},{"key":"2023013107190278100_B2","doi-asserted-by":"crossref","unstructured":"Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., Gibson, T.J. 1998Multiple sequence alignment with Clustal X. Trends Biochem. Sci.23403\u2013405","DOI":"10.1016\/S0968-0004(98)01285-7"},{"key":"2023013107190278100_B3","doi-asserted-by":"crossref","unstructured":"Pollard, D.A., Bergman, C.M., Stoye, J., Celniker, S.E., Eisen, M.B. 2004Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics56","DOI":"10.1186\/1471-2105-5-73"},{"key":"2023013107190278100_B4","doi-asserted-by":"crossref","unstructured":"Thompson, J.D., Plewniak, F., Pock, O. 1999A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res.272682\u20132690","DOI":"10.1093\/nar\/27.13.2682"},{"key":"2023013107190278100_B5","unstructured":"Yang, Z. 1997PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci.13555\u2013556"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/1\/122\/48961801\/bioinformatics_21_1_122.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/1\/122\/48961801\/bioinformatics_21_1_122.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T08:08:02Z","timestamp":1734509282000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/1\/122\/212369"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,8,13]]},"references-count":5,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2005,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth459","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2005,1,1]]},"published":{"date-parts":[[2004,8,13]]}}}