{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:20:48Z","timestamp":1764688848089},"reference-count":10,"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":1762,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Bisulfite sequencing, a combination of bisulfite treatment and high-throughput sequencing, has proved to be a valuable method for measuring DNA methylation at single base resolution. Here, we present B-SOLANA, an approach for the analysis of two-base encoding (colorspace) bisulfite sequencing data on the SOLiD platform of Life Technologies. It includes the alignment of bisulfite sequences and the determination of methylation levels in CpG as well as non-CpG sequence contexts. B-SOLANA enables a fast and accurate analysis of large raw sequence datasets.<\/jats:p>\n               <jats:p>Availability and implementation: The source code, released under the GNU GPLv3 licence, is freely available at http:\/\/code.google.com\/p\/bsolana\/.<\/jats:p>\n               <jats:p>Contact: \u00a0b.kreck@ikmb.uni-kiel.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr660","type":"journal-article","created":{"date-parts":[[2011,12,8]],"date-time":"2011-12-08T01:24:20Z","timestamp":1323307460000},"page":"428-429","source":"Crossref","is-referenced-by-count":23,"title":["B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data"],"prefix":"10.1093","volume":"28","author":[{"given":"Benjamin","family":"Kreck","sequence":"first","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany, 2Life Technologies, Advanced Sequencing Applications, Carlsbad, CA 92008, USA, 3Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany and 4Bioinformatics Group, The Babraham Institute, CB22 3AT Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Marnellos","sequence":"additional","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany, 2Life Technologies, Advanced Sequencing Applications, Carlsbad, CA 92008, USA, 3Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany and 4Bioinformatics Group, The Babraham Institute, CB22 3AT Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julia","family":"Richter","sequence":"additional","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany, 2Life Technologies, Advanced Sequencing Applications, Carlsbad, CA 92008, USA, 3Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany and 4Bioinformatics Group, The Babraham Institute, CB22 3AT Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Felix","family":"Krueger","sequence":"additional","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany, 2Life Technologies, Advanced Sequencing Applications, Carlsbad, CA 92008, USA, 3Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany and 4Bioinformatics Group, The Babraham Institute, CB22 3AT Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reiner","family":"Siebert","sequence":"additional","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany, 2Life Technologies, Advanced Sequencing Applications, Carlsbad, CA 92008, USA, 3Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany and 4Bioinformatics Group, The Babraham Institute, CB22 3AT Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andre","family":"Franke","sequence":"additional","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany, 2Life Technologies, Advanced Sequencing Applications, Carlsbad, CA 92008, USA, 3Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany and 4Bioinformatics Group, The Babraham Institute, CB22 3AT Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,12,6]]},"reference":[{"key":"2023012512170326400_B1","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1038\/nbt.1681","article-title":"Quantitative comparison of genome-wide DNA methylation mapping technologies","volume":"28","author":"Bock","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2023012512170326400_B2","doi-asserted-by":"crossref","first-page":"e9320","DOI":"10.1371\/journal.pone.0009320","article-title":"Whole methylome analysis by ultra-deep sequencing using two-base encoding","volume":"5","author":"Bormann","year":"2010","journal-title":"PLoS One"},{"key":"2023012512170326400_B3","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1038\/ng.865","article-title":"Increased methylation variation in epigenetic domains across cancer types","volume":"43","author":"Hansen","year":"2011","journal-title":"Nat. Genet."},{"key":"2023012512170326400_B4","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1126\/science.187.4173.226","article-title":"DNA modification mechanisms and gene activity during development","volume":"187","author":"Holliday","year":"1975","journal-title":"Science"},{"key":"2023012512170326400_B5","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":"2023012512170326400_B6","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nature08514","article-title":"Human DNA methylomes at base resolution show widespread epigenomic differences","volume":"462","author":"Lister","year":"2009","journal-title":"Nature"},{"key":"2023012512170326400_B7","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512170326400_B8","doi-asserted-by":"crossref","first-page":"1901","DOI":"10.1093\/bioinformatics\/btq291","article-title":"An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System","volume":"26","author":"Ondov","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512170326400_B9","doi-asserted-by":"crossref","first-page":"2435","DOI":"10.1093\/bioinformatics\/btr394","article-title":"MethylCoder: Software Pipeline for Bisulfite-Treated Sequences","volume":"27","author":"Pedersen","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512170326400_B10","doi-asserted-by":"crossref","first-page":"1994","DOI":"10.1016\/j.febslet.2010.10.061","article-title":"The DNA methylome","volume":"585","author":"Pelizzola","year":"2010","journal-title":"FEBS Lett."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/3\/428\/48879745\/bioinformatics_28_3_428.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/3\/428\/48879745\/bioinformatics_28_3_428.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:48:51Z","timestamp":1674658131000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/3\/428\/188595"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12,6]]},"references-count":10,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2012,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr660","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,2,1]]},"published":{"date-parts":[[2011,12,6]]}}}