{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T08:28:47Z","timestamp":1748939327558},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2298,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Bisulfite sequencing allows cytosine methylation, an important epigenetic marker, to be detected via nucleotide substitutions. Since the Applied Biosystems SOLiD System uses a unique di-base encoding that increases confidence in the detection of nucleotide substitutions, it is a potentially advantageous platform for this application. However, the di-base encoding also makes reads with many nucleotide substitutions difficult to align to a reference sequence with existing tools, preventing the platform's potential utility for bisulfite sequencing from being realized. Here, we present SOCS-B, a reference-based, un-gapped alignment algorithm for the SOLiD System that is tolerant of both bisulfite-induced nucleotide substitutions and a parametric number of sequencing errors, facilitating bisulfite sequencing on this platform. An implementation of the algorithm has been integrated with the previously reported SOCS alignment tool, and was used to align CpG methylation-enriched Arabidopsis thaliana bisulfite sequence data, exhibiting a 2-fold increase in sensitivity compared to existing methods for aligning SOLiD bisulfite data.<\/jats:p>\n               <jats:p>Availability: Executables, source code, and sample data are available at http:\/\/solidsoftwaretools.com\/gf\/project\/socs\/<\/jats:p>\n               <jats:p>Contact: \u00a0bergmann@nbacc.net<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq291","type":"journal-article","created":{"date-parts":[[2010,6,20]],"date-time":"2010-06-20T23:54:25Z","timestamp":1277078065000},"page":"1901-1902","source":"Crossref","is-referenced-by-count":19,"title":["An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System"],"prefix":"10.1093","volume":"26","author":[{"given":"Brian D.","family":"Ondov","sequence":"first","affiliation":[{"name":"1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, 2School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, 3Life Technologies, 850 Lincoln Centre Drive, Foster City, CA 94404 and 4Invitrogen, a division of Life Technologies Corporation, Genetic Systems Business Unit, 5791 Van Allen Way, Carlsbad, CA 92008, USA"},{"name":"1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, 2School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, 3Life Technologies, 850 Lincoln Centre Drive, Foster City, CA 94404 and 4Invitrogen, a division of Life Technologies Corporation, Genetic Systems Business Unit, 5791 Van Allen Way, Carlsbad, CA 92008, USA"}]},{"given":"Charles","family":"Cochran","sequence":"additional","affiliation":[{"name":"1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, 2School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, 3Life Technologies, 850 Lincoln Centre Drive, Foster City, CA 94404 and 4Invitrogen, a division of Life Technologies Corporation, Genetic Systems Business Unit, 5791 Van Allen Way, Carlsbad, CA 92008, USA"}]},{"given":"Mark","family":"Landers","sequence":"additional","affiliation":[{"name":"1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, 2School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, 3Life Technologies, 850 Lincoln Centre Drive, Foster City, CA 94404 and 4Invitrogen, a division of Life Technologies Corporation, Genetic Systems Business Unit, 5791 Van Allen Way, Carlsbad, CA 92008, USA"}]},{"given":"Gavin D.","family":"Meredith","sequence":"additional","affiliation":[{"name":"1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, 2School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, 3Life Technologies, 850 Lincoln Centre Drive, Foster City, CA 94404 and 4Invitrogen, a division of Life Technologies Corporation, Genetic Systems Business Unit, 5791 Van Allen Way, Carlsbad, CA 92008, USA"}]},{"given":"Miroslav","family":"Dudas","sequence":"additional","affiliation":[{"name":"1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, 2School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, 3Life Technologies, 850 Lincoln Centre Drive, Foster City, CA 94404 and 4Invitrogen, a division of Life Technologies Corporation, Genetic Systems Business Unit, 5791 Van Allen Way, Carlsbad, CA 92008, USA"}]},{"given":"Nicholas H.","family":"Bergman","sequence":"additional","affiliation":[{"name":"1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, 2School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, 3Life Technologies, 850 Lincoln Centre Drive, Foster City, CA 94404 and 4Invitrogen, a division of Life Technologies Corporation, Genetic Systems Business Unit, 5791 Van Allen Way, Carlsbad, CA 92008, USA"},{"name":"1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, 2School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, 3Life Technologies, 850 Lincoln Centre Drive, Foster City, CA 94404 and 4Invitrogen, a division of Life Technologies Corporation, Genetic Systems Business Unit, 5791 Van Allen Way, Carlsbad, CA 92008, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,6,18]]},"reference":[{"key":"2023012507594215200_B1","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nature06745","article-title":"Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning","volume":"452","author":"Cokus","year":"2008","journal-title":"Nature"},{"key":"2023012507594215200_B2","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1073\/pnas.89.5.1827","article-title":"A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands","volume":"89","author":"Frommer","year":"1992","journal-title":"Proc. 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