[Bioperl-l] what constitutes a good match?

[Tania Oh]

Hi All, 

I do apologise first if the question I ask is considered off topic.

I have some contig sequences which I want to match against the ensembl
protein database to see if I have any genes on my sequences. The question
is, when I do a blast against the ensembl.pep DB, what would consitute a
good match? If one was to only  use the pscore  (eg. 1e-60 for a
relatively good match) to sieve out potential genes on contigs, this would
cause the problem of missing out on fragments of genes with very high
pscores (eg. 0.5-3).

How have pple gotten around this problem? Any ideas on what constitutes a
good match? 

thanks in advance,
tania