{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T09:14:42Z","timestamp":1777108482092,"version":"3.51.4"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Current short read mapping programs are based on the reasonable premise that most sequencing errors occur near the 3\u2032 end of the read. These programs map reads with either a small number of mismatches in the entire read, or a small number of mismatches in the segment remaining after trimming bases from the 3\u2032 end or a single base from the 5\u2032 end. Though multiple sequencing errors most likely occur near the 3\u2032 end of the reads, they can still occur at the 5\u2032 end of the reads. Trimming from the 3\u2032 end will not be able to map these reads. We have developed a program, Maximum Oligonucleotide Mapping (MOM), based on the concept of query matching that is designed to capture a maximal length match within the short read satisfying the user defined error parameters. This query matching approach thus accommodates multiple sequencing errors at both ends. We demonstrate that this technique achieves greater sensitivity and a higher percentage of uniquely mapped reads when compared to existing programs such as SOAP, MAQ and SHRiMP.<\/jats:p>\n               <jats:p>Software and Test Data Availability: \u00a0http:\/\/mom.csbc.vcu.edu<\/jats:p>\n               <jats:p>Contact: \u00a0ygao@vcu.edu \u00a0hleaves@vcu.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp092","type":"journal-article","created":{"date-parts":[[2009,2,20]],"date-time":"2009-02-20T01:44:06Z","timestamp":1235094246000},"page":"969-970","source":"Crossref","is-referenced-by-count":36,"title":["MOM: maximum oligonucleotide mapping"],"prefix":"10.1093","volume":"25","author":[{"given":"Hugh L.","family":"Eaves","sequence":"first","affiliation":[{"name":"1 Center for the Study of Biological Complexity and 2Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan","family":"Gao","sequence":"additional","affiliation":[{"name":"1 Center for the Study of Biological Complexity and 2Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, USA"},{"name":"1 Center for the Study of Biological Complexity and 2Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,2,19]]},"reference":[{"key":"2023013110170718500_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023013110170718500_B2","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkn425","article-title":"Substantial biases in ultra-short read data sets from high-throughput DNA sequencing","author":"Dohm","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013110170718500_B3","first-page":"656","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023013110170718500_B4","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/bioinformatics\/btn025","article-title":"SOAP: short oligonucleotide alignment program","volume":"24","author":"Li","year":"2008","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/7\/969\/48984563\/bioinformatics_25_7_969.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/7\/969\/48984563\/bioinformatics_25_7_969.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:29:01Z","timestamp":1675189741000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/7\/969\/211463"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,19]]},"references-count":4,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2009,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp092","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,4,1]]},"published":{"date-parts":[[2009,2,19]]}}}