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Published online before print October 15, 2001, 10.1101/gr.195301
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Vol. 11, Issue 11, 1952-1957, November 2001

RESOURCES
Spidey: A Tool for mRNA-to-Genomic Alignments

Sarah J. Wheelan,1,2,3 Deanna M. Church,1 and James M. Ostell1

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA; 2 Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA

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.

3 Corresponding author.

11:1952-1957 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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