{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:49:54Z","timestamp":1773276594380,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Second-generation sequencing (SGS) generates millions of reads that need to be aligned to a reference genome allowing errors. Although current aligners can efficiently map reads allowing a small number of mismatches, they are not well suited for handling a large number of mismatches. The efficiency of aligners can be improved using various heuristics, but the sensitivity and accuracy of the alignments are sacrificed. In this article, we introduce Basic Alignment tool for Mismatches (BatMis)\u2014an efficient method to align short reads to a reference allowing k mismatches. BatMis is a Burrows\u2013Wheeler transformation based aligner that uses a seed and extend approach, and it is an exact method.<\/jats:p>\n               <jats:p>Results: Benchmark tests show that BatMis performs better than competing aligners in solving the k-mismatch problem. Furthermore, it can compete favorably even when compared with the heuristic modes of the other aligners. BatMis is a useful alternative for applications where fast k-mismatch mappings, unique mappings or multiple mappings of SGS data are required.<\/jats:p>\n               <jats:p>Availability and implementation: BatMis is written in C\/C++ and is freely available from http:\/\/code.google.com\/p\/batmis\/<\/jats:p>\n               <jats:p>Contact: \u00a0ksung@comp.nus.edu.sg<\/jats:p>\n               <jats:p>Supplementary Information: Supplementary information is available from Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts339","type":"journal-article","created":{"date-parts":[[2012,6,12]],"date-time":"2012-06-12T02:28:09Z","timestamp":1339468089000},"page":"2122-2128","source":"Crossref","is-referenced-by-count":32,"title":["BatMis: a fast algorithm for <i>k<\/i>-mismatch mapping"],"prefix":"10.1093","volume":"28","author":[{"given":"Chandana","family":"Tennakoon","sequence":"first","affiliation":[{"name":"1,2 \u00a01NUS Graduate School for Integrative Sciences and Engineering, (CeLS), #05-01, 28 Medical Drive, Singapore 117456 and 2Computational Biology Lab, School of Computing, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore"}]},{"given":"Rikky W.","family":"Purbojati","sequence":"additional","affiliation":[{"name":"1,2 \u00a01NUS Graduate School for Integrative Sciences and Engineering, (CeLS), #05-01, 28 Medical Drive, Singapore 117456 and 2Computational Biology Lab, School of Computing, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore"}]},{"given":"Wing-Kin","family":"Sung","sequence":"additional","affiliation":[{"name":"1,2 \u00a01NUS Graduate School for Integrative Sciences and Engineering, (CeLS), #05-01, 28 Medical Drive, Singapore 117456 and 2Computational Biology Lab, School of Computing, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore"}]}],"member":"286","published-online":{"date-parts":[[2012,6,10]]},"reference":[{"key":"2023012512533957700_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023012512533957700_B2","article-title":"A block-sorting lossless data compression algorithm","author":"Burrows","year":"1994","journal-title":"Technical report"},{"key":"2023012512533957700_B3","author":"Cox","year":"2006"},{"key":"2023012512533957700_B4","doi-asserted-by":"crossref","first-page":"e1000896","DOI":"10.1371\/journal.ppat.1000896","article-title":"Infidelity of sars-cov nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing","volume":"6","author":"Eckerle","year":"2010","journal-title":"PLoS pathogens"},{"key":"2023012512533957700_B5","article-title":"Opportunistic data structures with applications","author":"Ferragina","year":"2000","journal-title":"Technical report"},{"key":"2023012512533957700_B6","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/nmeth.1179","article-title":"Whole-genome sequencing and variant discovery in c. elegans.","volume":"5","author":"Hillier","year":"2008","journal-title":"Nat. Methods"},{"key":"2023012512533957700_B7","first-page":"31","article-title":"Practical aspects of compressed suffix arrays and fm-index in searching dna sequences","author":"Hon","year":"2004","journal-title":"ALENEX\/ANALC"},{"key":"2023012512533957700_B8","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1093\/bioinformatics\/btn032","article-title":"Compressed indexing and local alignment of dna","volume":"24","author":"Lam","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512533957700_B9","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short dna sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012512533957700_B10","doi-asserted-by":"crossref","first-page":"2431","DOI":"10.1093\/bioinformatics\/btn416","article-title":"Zoom! zillions of oligos mapped","volume":"24","author":"Lin","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512533957700_B11","first-page":"589","article-title":"Fast and accurate long-read alignment with burrows-wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012512533957700_B12","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short dna sequencing reads and calling variants using mapping quality scores","volume":"18","author":"Li","year":"2008","journal-title":"Genome Res."},{"key":"2023012512533957700_B13","first-page":"319","article-title":"Suffix arrays: a new method for on-line string searches","volume-title":"Proceedings of the first annual ACM-SIAM symposium on Discrete algorithms","author":"Manber","year":"1990"},{"key":"2023012512533957700_B14","doi-asserted-by":"crossref","first-page":"e1000256","DOI":"10.1371\/journal.pbio.1000256","article-title":"Zbed6, a novel transcription factor derived from a domesticated dna transposon regulates igf2 expression and muscle growth","volume":"7","author":"Markljung","year":"2009","journal-title":"PLoS Biol."},{"key":"2023012512533957700_B15","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nature06008","article-title":"Genome-wide maps of chromatin state in pluripotent and lineage-committed cells","volume":"448","author":"Mikkelsen","year":"2007","journal-title":"Nature"},{"key":"2023012512533957700_B16","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by rna-seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"2023012512533957700_B17","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"Tophat: discovering splice junctions with rna-seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512533957700_B18","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1101\/gr.088823.108","article-title":"Razersfast read mapping with sensitivity control","volume":"19","author":"Weese","year":"2009","journal-title":"Genome Research"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2122\/48872370\/bioinformatics_28_16_2122.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2122\/48872370\/bioinformatics_28_16_2122.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T17:52:14Z","timestamp":1674669134000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/16\/2122\/324101"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,10]]},"references-count":18,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2012,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts339","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,8,15]]},"published":{"date-parts":[[2012,6,10]]}}}