SPIDEY
Spidey is a prgram created by Sarah Wheelan. From the NCBI website: "Spidey was written with two main goals in mind: find good alignments regardless of intron size; and to avoid getting confused by nearby pseudogenes and paralogs. Towards the first goal, Spidey uses BLAST and Dot View (another local alignment tool) to find its alignments. Since these are both local alignment tools, Spidey does not intrinsically favor shorter or longer introns and has no maximum intron size. To avoid mistakenly including exons from paralogs and pseudogenes, Spidey first defines windows on the genomic sequence and then performs the mRNA-to-genomic alignment separately within each window. Because of the way the windows are constructed, neighboring paralogs or pseudogenes should be in separate windows and should not be included in the final spliced alignment."
See: Sarah J. Wheelan, Deanna M. Church, and James M. Ostell (2001) "Spidey: A Tool for mRNA-to-Genomic Alignments." Genome Res. 11(11):1952-57.
Manual: http://www.ncbi.nlm.nih.gov/spidey/spideydoc.html
INPUT = Nucleic Acid sequence files: One or more mRNA sequences (main input) and One or more Genomic sequences (input as a parameter).
Spidey is part of the NCBI Toolkit.
Format
Input is one or more mRNA probe sequences, which in the NGBW are supplied as primary input; and a genomic query sequence which is examined for intron and exon boundaries. Both sequences are in FASTA format.
Test Input Files:
Test Output Files: