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

By S. Wheelan, D. Church, James Ostell. Genome Research, 2001

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Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. (2003, background): “Several popular cDNA alignment programs are available for aligning ESTs and cDNAs to genomic sequences, including sim4 (10), gap2 (2), spidey (11), BLAT (12) and GeneSeqer (13).”
Current methods of gene prediction, their strengths and weaknesses. (2002, background): “Other available programs are AAT (66), GeneSeqer (67,68), SIM4 (69) and Spidey (70), all of which perform an alignment of the genomic DNA sequence against a cDNA database.”
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR (2004, methodology): “PerlPrimer uses the application Spidey (Wheelan et al., 2001) to find intron/exon boundaries, and screens all possible primer pairs against these data.”
A beginner's guide to eukaryotic genome annotation (2012, methodology): “For this reason, splice-site-aware alignment algorithms, such as Splign 44 , Spidey 45 , sim4 (REF.”