title: Spidey: a tool for mRNA-to-genomic alignments.
abstract: We have developed a computer program that aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing errors, or evolutionary divergence. We show how Spidey was used to align reference sequences to known genomic sequences and then to the draft human genome, to align mRNAs to gene clusters, and to align mouse mRNAs to human genomic sequence. We compared Spidey to two other spliced alignment programs; Spidey generally performed quite well in a very reasonable amount of time.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. wheelan@ncbi.nlm.nih.gov
authors.forename: S J
authors.initials: SJ
authors.lastname: Wheelan
authors.forename: D M
authors.initials: DM
authors.lastname: Church
authors.forename: J M
authors.initials: JM
authors.lastname: Ostell
mesh_terms: D000465:Algorithms; D000818:Animals; D004247:DNA / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D051379:Mice; D005810:Multigene Family / Q000235:genetics; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D013045:Species Specificity
chemical_list: D012333:RNA, Messenger; D004247:DNA