Spidey: A Tool for mRNA-to-Genomic Alignments

  1. Sarah J. Wheelan1,2,3,
  2. Deanna M. Church1, and
  3. James M. Ostell1
  1. 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA; 2Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA

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.

Footnotes

  • ↵3 Corresponding author.

  • E-MAIL wheelan{at}ncbi.nlm.nih.gov; FAX (301) 480-2288.

  • Article published on-line before print: Genome Res.,10.1101/gr.195301.

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.195301.

    • Received May 3, 2001.
    • Accepted July 30, 2001.
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  1. Published in Advance October 15, 2001, doi: 10.1101/gr.195301 Genome Res. 11: 1952-1957 Cold Spring Harbor Laboratory Press

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