title: A computer program for aligning a cDNA sequence with a genomic DNA sequence.
abstract: We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number of sequencing errors. A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation.
authors.affiliation: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 USA.
authors.forename: L
authors.initials: L
authors.lastname: Florea
authors.forename: G
authors.initials: G
authors.lastname: Hartzell
authors.forename: Z
authors.initials: Z
authors.lastname: Zhang
authors.forename: G M
authors.initials: GM
authors.lastname: Rubin
authors.forename: W
authors.initials: W
authors.lastname: Miller
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D004247:DNA / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics; D020224:Expressed Sequence Tags; D016678:Genome; D006801:Humans; D051379:Mice; D012333:RNA, Messenger / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D004247:DNA