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Comparative Study
. 2001 Nov;11(11):1952-7.
doi: 10.1101/gr.195301.

Spidey: a tool for mRNA-to-genomic alignments

S J Wheelan  1 , D M Church, J M Ostell
Affiliations
Comparative Study

Spidey: a tool for mRNA-to-genomic alignments

S J Wheelan et al. Genome Res. 2001 Nov.

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.

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Figures

Figure 1
Figure 1
The top three Spidey models for the alignment of BIRC1 to its genomic sequence, as seen in Ingenue (a sequence and alignment workbench by F. Aklilu, unpubl.)
Figure 2
Figure 2
Mouse NM_010880 (nucleolin) aligned to human M60858, shown in Ingenue with the annotated mRNA from the human sequence. The top line shows the human sequence, the center line represent the annotated human mRNA, and the bottom line shows the Spidey model for the mouse mRNA.
See this image and copyright information in PMC

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