Spidey: A tool for mRNA-to-genomic alignments

Sarah J. Wheelan, Deanna M. Church, James M. Ostell

Research output: Contribution to journalArticlepeer-review

249 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1952-1957
Number of pages6
JournalGenome research
Issue number11
StatePublished - 2001

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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