{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:36:33Z","timestamp":1773275793024,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Multi-mapping sequence tags are a significant impediment to short-read sequencing platforms. These tags are routinely omitted from further analysis, leading to experimental bias and reduced coverage. Here, we present MuMRescueLite, a low-resource requirement version of the MuMRescue software that has been used by several next generation sequencing projects to probabilistically reincorporate multi-mapping tags into mapped short read data.<\/jats:p>\n               <jats:p>Availability and implementation: MuMRescueLite is written in Python; executables and documentation are available from http:\/\/genome.gsc.riken.jp\/osc\/english\/software\/.<\/jats:p>\n               <jats:p>Contact: \u00a0geoff.faulkner@roslin.ed.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp438","type":"journal-article","created":{"date-parts":[[2009,7,16]],"date-time":"2009-07-16T00:49:46Z","timestamp":1247705386000},"page":"2613-2614","source":"Crossref","is-referenced-by-count":35,"title":["Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite"],"prefix":"10.1093","volume":"25","author":[{"given":"Takehiro","family":"Hashimoto","sequence":"first","affiliation":[{"name":"1 Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan, 2Expression Genomics Laboratory, Institute for Molecular Bioscience, University of Queensland, QLD, 4072, Australia and 3Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, Scotland, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michiel J.L.","family":"de Hoon","sequence":"additional","affiliation":[{"name":"1 Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan, 2Expression Genomics Laboratory, Institute for Molecular Bioscience, University of Queensland, QLD, 4072, Australia and 3Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, Scotland, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sean M.","family":"Grimmond","sequence":"additional","affiliation":[{"name":"1 Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan, 2Expression Genomics Laboratory, Institute for Molecular Bioscience, University of Queensland, QLD, 4072, Australia and 3Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, Scotland, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carsten O.","family":"Daub","sequence":"additional","affiliation":[{"name":"1 Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan, 2Expression Genomics Laboratory, Institute for Molecular Bioscience, University of Queensland, QLD, 4072, Australia and 3Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, Scotland, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoshihide","family":"Hayashizaki","sequence":"additional","affiliation":[{"name":"1 Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan, 2Expression Genomics Laboratory, Institute for Molecular Bioscience, University of Queensland, QLD, 4072, Australia and 3Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, Scotland, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geoffrey J.","family":"Faulkner","sequence":"additional","affiliation":[{"name":"1 Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan, 2Expression Genomics Laboratory, Institute for Molecular Bioscience, University of Queensland, QLD, 4072, Australia and 3Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, Scotland, UK"},{"name":"1 Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan, 2Expression Genomics Laboratory, Institute for Molecular Bioscience, University of Queensland, QLD, 4072, Australia and 3Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, Scotland, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,7,15]]},"reference":[{"key":"2023013112124996700_B1","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project","volume":"447","author":"Birney","year":"2007","journal-title":"Nature"},{"key":"2023013112124996700_B2","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/ng1789","article-title":"Genome-wide analysis of mammalian promoter architecture and evolution","volume":"38","author":"Carninci","year":"2006","journal-title":"Nat. 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