{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T22:10:51Z","timestamp":1675203051985},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Haplotype assembly is becoming a very important tool in genome sequencing of human and other organisms. Although haplotypes were previously inferred from genome assemblies, there has never been a comparative haplotype browser that depicts a global picture of whole-genome alignments among haplotypes of different organisms. We introduce a whole-genome HAPLotype brOWSER (HAPLOWSER), providing evolutionary perspectives from multiple aligned haplotypes and functional annotations. Haplowser enables the comparison of haplotypes from metagenomes, and associates conserved regions or the bases at the conserved regions with functional annotations and custom tracks. The associations are quantified for further analysis and presented as pie charts. Functional annotations and custom tracks that are projected onto haplotypes are saved as multiple files in FASTA format. Haplowser provides a user-friendly interface, and can display alignments of haplotypes with functional annotations at any resolution.<\/jats:p>\n               <jats:p>Availability: Haplowser, written in Java, supports multiple platforms including Windows and Linux. Haplowser is publicly available at http:\/\/embio.yonsei.ac.kr\/haplowser<\/jats:p>\n               <jats:p>Contact: \u00a0sanghyun@cs.yonsei.ac.kr; lilei@usc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at http:\/\/embio.yonsei.ac.kr\/haplowser<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp399","type":"journal-article","created":{"date-parts":[[2009,6,28]],"date-time":"2009-06-28T00:13:44Z","timestamp":1246148024000},"page":"2430-2431","source":"Crossref","is-referenced-by-count":2,"title":["HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome"],"prefix":"10.1093","volume":"25","author":[{"given":"Jong Hyun","family":"Kim","sequence":"first","affiliation":[{"name":"1 Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA, 2Department of Computer Science, Yonsei University, 134 Shinchon-dong, Seoul, 120-749, Republic of Korea and 3Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1050 Childs way, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Woo-Cheol","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA, 2Department of Computer Science, Yonsei University, 134 Shinchon-dong, Seoul, 120-749, Republic of Korea and 3Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1050 Childs way, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael S.","family":"Waterman","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA, 2Department of Computer Science, Yonsei University, 134 Shinchon-dong, Seoul, 120-749, Republic of Korea and 3Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1050 Childs way, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanghyun","family":"Park","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA, 2Department of Computer Science, Yonsei University, 134 Shinchon-dong, Seoul, 120-749, Republic of Korea and 3Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1050 Childs way, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei M.","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA, 2Department of Computer Science, Yonsei University, 134 Shinchon-dong, Seoul, 120-749, Republic of Korea and 3Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1050 Childs way, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,6,27]]},"reference":[{"key":"2023013112121540400_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: A new generation of protein database search program","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023013112121540400_B2","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1101\/gr.789803","article-title":"AVID: a global alignment program","volume":"13","author":"Bray","year":"2003","journal-title":"Genome Res."},{"key":"2023013112121540400_B3","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100040","article-title":"The personal genome project","volume":"1","author":"Church","year":"2005","journal-title":"Mol. 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