[Bioperl-l] translate DNA whith unkown ORF

[Chris]

Hello,

I have a fasta file of coding exon DNA. The problem is each sequence is not
a full coding exon, but may be only a segment of an exon. I would like to
translate this DNA to protein, but the ORF is unknown. I can see the actual
protein sequence on the UCSC browser but when I only have segments of  exons
there is no way to download the protein sequence segments, just the sequence
for the whole gene. Does anybody know a way I can access this protein
sequence, given a bed file of the coordinates of the coding sequence
segments? I have tried the script "longorf.pl" on the fasta file of the DNA
sequence but this does not work (or I cannot get it to) - I think it looks
for an atg in the sequence and assumes that is the start codon..

Thanks,
Chris.