{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,13]],"date-time":"2025-09-13T16:24:23Z","timestamp":1757780663091},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The sequencing of bisulfite-treated DNA (Bi-Seq) is becoming a gold standard for methylation studies. The mapping of Bi-Seq reads is complex and requires special alignment algorithms. This problem is particularly relevant for SOLiD color space, where the bisulfite conversion C\/T changes two adjacent colors into 16 possible combinations. Here, we present an algorithm that efficiently aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands.<\/jats:p>\n               <jats:p>Availability and implementation: The algorithm has been implemented as an option of the program PASS, freely available at http:\/\/pass.cribi.unipd.it.<\/jats:p>\n               <jats:p>Contact: \u00a0pass@cribi.unipd.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts675","type":"journal-article","created":{"date-parts":[[2012,11,18]],"date-time":"2012-11-18T02:50:02Z","timestamp":1353207002000},"page":"268-270","source":"Crossref","is-referenced-by-count":11,"title":["PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads"],"prefix":"10.1093","volume":"29","author":[{"given":"Davide","family":"Campagna","sequence":"first","affiliation":[{"name":"1 CRIBI Biotechnology Centre and 2Department of Biology, Universit\u00e0 di Padova, 35131 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Telatin","sequence":"additional","affiliation":[{"name":"1 CRIBI Biotechnology Centre and 2Department of Biology, Universit\u00e0 di Padova, 35131 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudio","family":"Forcato","sequence":"additional","affiliation":[{"name":"1 CRIBI Biotechnology Centre and 2Department of Biology, Universit\u00e0 di Padova, 35131 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicola","family":"Vitulo","sequence":"additional","affiliation":[{"name":"1 CRIBI Biotechnology Centre and 2Department of Biology, Universit\u00e0 di Padova, 35131 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giorgio","family":"Valle","sequence":"additional","affiliation":[{"name":"1 CRIBI Biotechnology Centre and 2Department of 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