{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T14:46:55Z","timestamp":1774018015334,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra high-throughput sequencing machines. With a carefully designed index-filtering algorithm and an efficient implementation, SeqMap can map tens of millions of short sequences to a genome of several billions of nucleotides. Multiple substitutions and insertions\/deletions of the nucleotide bases in the sequences can be tolerated and therefore detected. SeqMap supports FASTA input format and various output formats, and provides command line options for tuning almost every aspect of the mapping process. A typical mapping can be done in a few hours on a desktop PC. Parallel use of SeqMap on a cluster is also very straightforward.<\/jats:p>\n               <jats:p>Contact: \u00a0whwong@stanford.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn429","type":"journal-article","created":{"date-parts":[[2008,8,13]],"date-time":"2008-08-13T02:35:24Z","timestamp":1218594924000},"page":"2395-2396","source":"Crossref","is-referenced-by-count":400,"title":["SeqMap: mapping massive amount of oligonucleotides to the genome"],"prefix":"10.1093","volume":"24","author":[{"given":"Hui","family":"Jiang","sequence":"first","affiliation":[{"name":"1 Institute for Computational and Mathematical Engineering and 2Department of Statistics, Stanford University, Stanford, California 94305, USA"}]},{"given":"Wing Hung","family":"Wong","sequence":"additional","affiliation":[{"name":"1 Institute for Computational and Mathematical Engineering and 2Department of Statistics, Stanford University, Stanford, California 94305, USA"}]}],"member":"286","published-online":{"date-parts":[[2008,8,12]]},"reference":[{"key":"2023020211255407600_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":"2023020211255407600_B2","first-page":"656","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023020211255407600_B3","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"},{"key":"2023020211255407600_B4","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1145\/1242572.1242592","article-title":"Detecting near-duplicates for web crawling","volume-title":"Proceedings of the 16th international conference on World Wide Web","author":"Manku","year":"2007"},{"key":"2023020211255407600_B5","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":"2023020211255407600_B6","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/1471-2105-9-128","article-title":"Using quality scores and longer reads improves accuracy of Solexa read mapping","volume":"9","author":"Smith","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023020211255407600_B7","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1261\/rna.1070208","article-title":"MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays","volume":"14","author":"Xing","year":"2008","journal-title":"RNA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/20\/2395\/49052170\/bioinformatics_24_20_2395.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/20\/2395\/49052170\/bioinformatics_24_20_2395.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T11:28:36Z","timestamp":1675337316000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/20\/2395\/258850"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,8,12]]},"references-count":7,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2008,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn429","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,10,15]]},"published":{"date-parts":[[2008,8,12]]}}}