{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T06:06:01Z","timestamp":1744178761728},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2116,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can be further analyzed. Current fast and memory-saving short-read mappers could give us a quick view of the transcriptome. However, they are neither designed for reads that span across splice junctions nor for repetitive reads, which can be mapped to multiple locations in the genome (multi-reads). Here, we describe a new software package: ABMapper, which is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature.<\/jats:p>\n               <jats:p>Availability and Implementation: The software is freely available at: http:\/\/abmapper.sourceforge.net\/. The software is written in C++ and PERL. It runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.<\/jats:p>\n               <jats:p>Contact: \u00a0tf.chan@cuhk.edu.hk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq656","type":"journal-article","created":{"date-parts":[[2010,12,18]],"date-time":"2010-12-18T03:20:38Z","timestamp":1292642438000},"page":"421-422","source":"Crossref","is-referenced-by-count":11,"title":["ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping"],"prefix":"10.1093","volume":"27","author":[{"given":"Shao-Ke","family":"Lou","sequence":"first","affiliation":[{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"},{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"},{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"}]},{"given":"Bing","family":"Ni","sequence":"additional","affiliation":[{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"}]},{"given":"Leung-Yau","family":"Lo","sequence":"additional","affiliation":[{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"}]},{"given":"Stephen Kwok-Wing","family":"Tsui","sequence":"additional","affiliation":[{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"},{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"}]},{"given":"Ting-Fung","family":"Chan","sequence":"additional","affiliation":[{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"},{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"}]},{"given":"Kwong-Sak","family":"Leung","sequence":"additional","affiliation":[{"name":"1 Hong Kong Bioinformatics Centre, 2School of Life Sciences, 3Department of Computer Science and Engineering, and 4School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin NT, Hong Kong SAR"}]}],"member":"286","published-online":{"date-parts":[[2010,12,17]]},"reference":[{"key":"2023012511534505400_B1","doi-asserted-by":"crossref","first-page":"R34","DOI":"10.1186\/gb-2010-11-3-r34","article-title":"Global and unbiased detection of splice junctions from RNA-seq data","volume":"11","author":"Ameur","year":"2010","journal-title":"Genome Biol."},{"key":"2023012511534505400_B2","doi-asserted-by":"crossref","first-page":"4570","DOI":"10.1093\/nar\/gkq211","article-title":"Detection of splice junctions from paired-end RNA-seq data by SpliceMap","volume":"38","author":"Au","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012511534505400_B3","article-title":"A block-sorting lossless data compression algorithm","volume-title":"Technical Report 124","author":"Burrows","year":"1994"},{"key":"2023012511534505400_B4","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":"2023012511534505400_B5","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511534505400_B6","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":"2023012511534505400_B7","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2023012511534505400_B8","doi-asserted-by":"crossref","first-page":"e1000843","DOI":"10.1371\/journal.pcbi.1000843","article-title":"Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq","volume":"6","author":"Xu","year":"2010","journal-title":"PLoS Comput. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/3\/421\/48862530\/bioinformatics_27_3_421.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/3\/421\/48862530\/bioinformatics_27_3_421.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T12:00:55Z","timestamp":1674648055000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/3\/421\/319727"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,12,17]]},"references-count":8,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2011,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq656","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,2,1]]},"published":{"date-parts":[[2010,12,17]]}}}