{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:24:48Z","timestamp":1761488688547},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The large number of genomes that will be sequenced will need to be annotated with genes and other functional features. Aligning gene sequences from a related species to the target genome is an economical and highly reliable method to identify genes; unfortunately, existing tools have been lacking in sensitivity and speed. A program we reported, sim4cc, was shown to be highly accurate but is limited to comparing one cDNA with one genomic sequence. We present here an optimization of the tool, implemented in the packages sim4db and leaff. The new tool performs batch alignments of cDNA and genomic sequences in a fraction of the time required by its predecessor, and thus is very well suited for genome-wide analyses.<\/jats:p>\n               <jats:p>Availability: \u00a0Sim4db and leaff are written in C, C++ and Perl for Linux and other Unix platforms. Source code is distributed free of charge from http:\/\/sourceforge.net\/projects\/kmer\/.<\/jats:p>\n               <jats:p>Contact: \u00a0florea@umiacs.umd.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics Online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr285","type":"journal-article","created":{"date-parts":[[2011,5,7]],"date-time":"2011-05-07T00:34:56Z","timestamp":1304728496000},"page":"1869-1870","source":"Crossref","is-referenced-by-count":18,"title":["<tt>Sim4db<\/tt> and <tt>Leaff<\/tt>: utilities for fast batch spliced alignment and sequence indexing"],"prefix":"10.1093","volume":"27","author":[{"given":"Brian","family":"Walenz","sequence":"first","affiliation":[{"name":"1 The J. Craig Venter Institute, Rockville, MD 20850 and 2Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA"}]},{"given":"Liliana","family":"Florea","sequence":"additional","affiliation":[{"name":"1 The J. Craig Venter Institute, Rockville, MD 20850 and 2Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,5,6]]},"reference":[{"key":"2023012512014284600_B1","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1101\/gr.8.9.967","article-title":"A computer program for aligning a cDNA sequence with a genomic DNA sequence","volume":"8","author":"Florea","year":"1998","journal-title":"Genome Res."},{"key":"2023012512014284600_B2","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1093\/jhered\/esp086","article-title":"Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species","volume":"100","author":"Genome 10K Community of Scientists","year":"2009","journal-title":"J. Hered."},{"key":"2023012512014284600_B3","first-page":"656","article-title":"BLAT \u2013 the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012512014284600_B4","doi-asserted-by":"crossref","first-page":"e1000475","DOI":"10.1371\/journal.pbio.1000475","article-title":"Changing the landscape of genome sequencing: the domestic turkey (Meleagris gallopavo) genome assembly and analysis","volume":"8","author":"Turkey Genome Sequencing Consortium","year":"2010","journal-title":"PLoS Biol."},{"key":"2023012512014284600_B5","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1093\/bioinformatics\/bti310","article-title":"GMAP: a genomic mapping and alignment program for mRNA and EST sequences","volume":"21","author":"Wu","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012512014284600_B6","doi-asserted-by":"crossref","first-page":"e80","DOI":"10.1093\/nar\/gkp319","article-title":"Sim4cc: a cross-species spliced alignment program","volume":"37","author":"Zhou","year":"2009","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/13\/1869\/48874633\/bioinformatics_27_13_1869.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/13\/1869\/48874633\/bioinformatics_27_13_1869.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:12:53Z","timestamp":1674655973000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/13\/1869\/185389"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,6]]},"references-count":6,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2011,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr285","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,7,1]]},"published":{"date-parts":[[2011,5,6]]}}}