[Bioperl-l] Discovering new genes

[Affan Qureshi]

Hi,
This is a newbie question, maybe not directly related to BioPerl even.

I am a student working on a set of newly discovered DNA sequence files for
an organism. I would like to know the steps involved in discovering and
analyzing the DNA sequences. I want to classify the various functional
units in the genes represented by the DNA sequences.

I have conducted a Blastx search for all the 100 files and have found some
very good matches (e.g e-value 1e-120). I have seperated out the big match
sequences in a seperate file. I want to know what the next steps are.
Maybe I should compare the matched sequences(proteins) against the
corresponding ones in other organisms like Yeast, worm, drosophila etc and
find out whether there is a similarity between the neighboring proteins. I
tried doing this at SPRING website and looked up the matches on SWISS-PROT
etc.

I thought since you guys are experienced bioinformaticists and do this
type of work every day, maybe you could give me some pointers.

Sorry about the off-topic question.

Thanks,

Affan