{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T14:56:42Z","timestamp":1785337002314,"version":"3.55.0"},"reference-count":23,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2006,6,23]],"date-time":"2006-06-23T00:00:00Z","timestamp":1151020800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.0020073","type":"journal-article","created":{"date-parts":[[2006,6,20]],"date-time":"2006-06-20T15:51:37Z","timestamp":1150818697000},"page":"e73","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":29,"title":["Parametric Alignment of Drosophila Genomes"],"prefix":"10.1371","volume":"2","author":[{"given":"Colin N","family":"Dewey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter M","family":"Huggins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Woods","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernd","family":"Sturmfels","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lior","family":"Pachter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2006,6,23]]},"reference":[{"key":"pcbi-0020073-b001","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the amino acid sequence of two proteins.","volume":"48","year":"1970","journal-title":"J Mol Biol"},{"key":"pcbi-0020073-b002","first-page":"D390","article-title":"Flybase: Genes and gene models.","volume":"33","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0020073-b003","doi-asserted-by":"crossref","first-page":"3525","DOI":"10.1093\/nar\/gkg623","article-title":"MAVID multiple alignment server.","volume":"31","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0020073-b004","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1101\/gr.809403","article-title":"Human\u2013mouse alignments with BLASTZ.","volume":"13","year":"2003","journal-title":"Genome Res"},{"key":"pcbi-0020073-b005","doi-asserted-by":"crossref","first-page":"6090","DOI":"10.1073\/pnas.89.13.6090","article-title":"Parametric sequence comparisons.","volume":"89","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0020073-b006","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1007\/BF01185430","article-title":"Parametric optimization of sequence alignment.","volume":"12","year":"1994","journal-title":"Algorithmica"},{"key":"pcbi-0020073-b007","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/S0076-6879(96)66030-3","article-title":"Parametric and inverse\u2013parametric sequence alignment with XPARAL.","volume":"266","year":"1996","journal-title":"Methods Enzymol"},{"key":"pcbi-0020073-b008","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/S1570-8667(03)00078-9","article-title":"Parametric multiple sequence alignment and phylogeny construction.","volume":"2","year":"2004","journal-title":"J Discrete Algorithms"},{"key":"pcbi-0020073-b009","first-page":"271","article-title":"Parametric sequence alignment.","volume":"(Volume 2)","year":"2005","journal-title":"Handbook of computational molecular biology"},{"key":"pcbi-0020073-b010","doi-asserted-by":"crossref","first-page":"16138","DOI":"10.1073\/pnas.0406011101","article-title":"Parametric inference for biological sequence analysis.","volume":"101","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0020073-b011","doi-asserted-by":"crossref","unstructured":"Pachter\n\t\t\t\t\t\t\tL\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tSturmfels\n\t\t\t\t\t\t\tB\n\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t2005\n\t\t\t\t\tAlgebraic statistics for computational biology\n\t\t\t\t\tCambridge\n\t\t\t\t\tCambridge University Press\n\t\t\t\t\t420\n\t\t\t\t\tp.","DOI":"10.1017\/CBO9780511610684"},{"key":"pcbi-0020073-b012","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/nature02426","article-title":"Genome sequence of the Brown Norway rat yields insights into mammalian evolution.","volume":"428","year":"2004","journal-title":"Nature"},{"key":"pcbi-0020073-b013","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/nature01262","article-title":"Initial sequencing and comparative analysis of the mouse genome.","volume":"420","year":"2002","journal-title":"Nature"},{"key":"pcbi-0020073-b014","unstructured":"Dewey\n\t\t\t\t\t\t\tC\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tPachter\n\t\t\t\t\t\t\tL\n\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t2006\n\t\t\t\t\tMercator: Multiple whole-genome orthology map construction\n\t\t\t\t\tAvailable: http:\/\/bio.math.berkeley.edu\/mercator\/. Accessed 22 May 2006."},{"key":"pcbi-0020073-b015","first-page":"656","article-title":"BLAT\u2014The BLAST like alignment tool.","volume":"12","year":"2002","journal-title":"Genome Biol"},{"key":"pcbi-0020073-b016","doi-asserted-by":"crossref","unstructured":"Durbin\n\t\t\t\t\t\t\tR\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tEddy\n\t\t\t\t\t\t\tS\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tKorgh\n\t\t\t\t\t\t\tA\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tMitchison\n\t\t\t\t\t\t\tG\n\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t1998\n\t\t\t\t\tBiological sequence analysis: Probabilistic models of proteins and nucleic acids\n\t\t\t\t\tCambridge\n\t\t\t\t\tCambridge University Press\n\t\t\t\t\t356\n\t\t\t\t\tp.","DOI":"10.1017\/CBO9780511790492"},{"key":"pcbi-0020073-b017","unstructured":"Chiaromonte\n\t\t\t\t\t\t\tF\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tYap\n\t\t\t\t\t\t\tV\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tMiller\n\t\t\t\t\t\t\tW\n\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t2002\n\t\t\t\t\tScoring pairwise genomic sequence alignments.\n\t\t\t\t\tIn:\n\t\t\t\t\tProceedings of the Pacific Symposium on Biocomputing\n\t\t\t\t\tpp.\n\t\t\t\t\t115\n\t\t\t\t\t126"},{"key":"pcbi-0020073-b018","doi-asserted-by":"crossref","unstructured":"Gr\u00fcnbaum\n\t\t\t\t\t\t\tB\n\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t2003\n\t\t\t\t\tConvex polytopes.\n\t\t\t\t\tIn:\n\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tKaibel\n\t\t\t\t\t\t\tV\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tKlee\n\t\t\t\t\t\t\t V\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tZiegler\n\t\t\t\t\t\t\tGM\n\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\tGraduate texts in mathematics\n\t\t\t\t\t(Volume 221)\n\t\t\t\t\t2nd edition.\n\t\t\t\t\tNew York\n\t\t\t\t\tSpringer-Verlag\n\t\t\t\t\t468\n\t\t\t\t\tp.","DOI":"10.1007\/978-1-4613-0019-9"},{"key":"pcbi-0020073-b019","doi-asserted-by":"crossref","unstructured":"Preparata F, Shamos M\n\t\t\t\t\t1985\n\t\t\t\t\tComputational geometry: An introduction.\n\t\t\t\t\tIn:\n\t\t\t\t\tTexts and monographs in computer science\n\t\t\t\t\tNew York\n\t\t\t\t\tSpringer\n\t\t\t\t\t390\n\t\t\t\t\t p.","DOI":"10.1007\/978-1-4612-1098-6_1"},{"key":"pcbi-0020073-b020","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.3059305","article-title":"Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution.","volume":"15","year":"2005","journal-title":"Genome Res"},{"key":"pcbi-0020073-b021","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1093\/bioinformatics\/bti173","article-title":"Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, D. melanogaster.","volume":"21","year":"2005","journal-title":"Bioinformatics"},{"key":"pcbi-0020073-b022","doi-asserted-by":"crossref","unstructured":"Jukes\n\t\t\t\t\t\t\tT\n\t\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tCantor\n\t\t\t\t\t\t\tC\n\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\t1969\n\t\t\t\t\tEvolution of protein molecules.\n\t\t\t\t\tIn:\n\t\t\t\t\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t\tMunro\n\t\t\t\t\t\t\tH\n\t\t\t\t\t\t\n\t\t\t\t\t\n\t\t\t\t\tMammalian protein metabolism\n\t\t\t\t\tNew York\n\t\t\t\t\tAcademic Press\n\t\t\t\t\tpp.\n\t\t\t\t\t21\n\t\t\t\t\t32","DOI":"10.1016\/B978-1-4832-3211-9.50009-7"},{"key":"pcbi-0020073-b023","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1093\/nar\/27.11.2369","article-title":"Alignment of whole genomes.","volume":"27","year":"1999","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0020073","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T21:41:46Z","timestamp":1588801306000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0020073"}},"subtitle":[],"editor":[{"given":"Dan","family":"Gusfield","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2006,6,23]]},"references-count":23,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2006,6,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0020073","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,6,23]]}}}