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Genome Res. 2001 Nov;11(11):1952-7.

Spidey: a tool for mRNA-to-genomic alignments.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. wheelan@ncbi.nlm.nih.gov

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.

PMID:
11691860
PMCID:
PMC311166
DOI:
10.1101/gr.195301
[Indexed for MEDLINE]
Free PMC Article

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