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rnaspl_to_fplot

Usage: [-e -q] rnaspl_to_fplot <Seq.rnaspl >Seq.rnaspl.fplot

This program reformats the output from RNASPL as a fplot file. RNASPL finds exon-exon boundaries in cDNA. It can be access through an email server: mailx -s rnaspl service@bchs.uh.edu < test.seq mailx -s rnaspl services@bioinformatics.weizmann.ac.il < test.seq

Note that the RNASPL program can't handle N's in the sequence--it just strips them out and runs on the shortened sequence. As a work-around, replace all the N's with another bp, such as 'Y' using cutdna:

cutdna 1 end -mY <Dna.with.Ns >Dna.with.Ys

Reference for RNASPL: Solovyev V.V.,Salamov A.A., Lawrence C.B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. (Nucl.Acids Res.,1994,22,24,5156-5163).

The RNASPL file is read from standard input, and the fplot file is written to standard output.

Switches:

-e# Set the minimum exon size. If set to zero, all the results from RNASPL will be displayed, and with exons and gaps shown with tick marks. Default is a minimum exon size of 50 bp.

-q Print out this help information.

Last modified 6-8-99.

Written by Jim Lund in the lab of Roger Reeves, Johns Hopkins University