{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T18:08:28Z","timestamp":1776794908905,"version":"3.51.2"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2609,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"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: The Pine Alignment and SNP Identification Pipeline (PineSAP) provides a high-throughput solution to single nucleotide polymorphism (SNP) prediction using multiple sequence alignments from re-sequencing data. This pipeline integrates a hybrid of customized scripting, existing utilities and machine learning in order to increase the speed and accuracy of SNP calls. The implementation of this pipeline results in significantly improved multiple sequence alignments and SNP identifications when compared with existing solutions. The use of machine learning in the SNP identifications extends the pipeline's application to any eukaryotic species where full genome sequence information is unavailable.<\/jats:p>\n               <jats:p>Availability: All code used for this pipeline is freely available at the Dendrome project website (http:\/\/dendrome.ucdavis.edu\/adept2\/resequencing.html)<\/jats:p>\n               <jats:p>Contact: \u00a0jlwegrzyn@ucdavis.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp477","type":"journal-article","created":{"date-parts":[[2009,8,11]],"date-time":"2009-08-11T01:06:19Z","timestamp":1249952779000},"page":"2609-2610","source":"Crossref","is-referenced-by-count":26,"title":["PineSAP\u2014sequence alignment and SNP identification pipeline"],"prefix":"10.1093","volume":"25","author":[{"given":"Jill L.","family":"Wegrzyn","sequence":"first","affiliation":[{"name":"1 Department of Plant Sciences and 2Department of Evolution and Ecology, Address One Shields Ave. University of California, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer M.","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Department of Plant Sciences and 2Department of Evolution and Ecology, Address One Shields Ave. University of California, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Liechty","sequence":"additional","affiliation":[{"name":"1 Department of Plant Sciences and 2Department of Evolution and Ecology, Address One Shields Ave. University of California, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David B.","family":"Neale","sequence":"additional","affiliation":[{"name":"1 Department of Plant Sciences and 2Department of Evolution and Ecology, Address One Shields Ave. University of California, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,8,10]]},"reference":[{"key":"2023013112123635900_B1","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1093\/bioinformatics\/btm389","article-title":"DNA reference alignment benchmarks based on tertiary structure of encoded proteins","volume":"23","author":"Carroll","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112123635900_B2","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1101\/gr.2821705","article-title":"ProbCons: probabilistic consistency-based multiple sequence alignment","volume":"15","author":"Do","year":"2005","journal-title":"Genome Res."},{"key":"2023013112123635900_B3","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1101\/gr.8.3.175","article-title":"Base-calling of automated sequencer traces using phred. 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