A computer program for aligning a cDNA sequence with a genomic DNA sequence.
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.
Florea
L
L
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 USA.
Hartzell
G
G
Zhang
Z
Z
Rubin
G M
GM
Miller
W
W
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
D018076:DNA, Complementary; D012333:RNA, Messenger; D004247:DNA