Perl programming sequence

Question

[titoo]

Hello,

I have a set of 156 dna sequences (fasta format).

 - ">123 ATCGATCGATGC
 - ">124 ATCGATCGATGC
 - ">125 ATCGATCGATGC
 - ...........

i want to execute an online application of sequence analysis "WEEDER" ?

for each DNA sequence i want to extract all octamer (8 pb) composition. for exemple ">123 ATCGATCGATGC"

• ATCGATCG
• TCGATCGA
• CGATCGAT
• GATCGATG
• ATCGATGC

then, for each DNA sequence i want to analyse it in weeder. after obtaining result, i want to atribute the score to the list of motifs composition.(attribution in both strand)

• ATCGATCG 12.11
• TCGATCGA 11.33
• CGATCGAT 12.11
• GATCGATG 10.35
• ATCGATGC 0 (when we dont have score attribut a 0)

thank you

[Pierre Lindenbaum]

what is the question ?

[titoo]

i ask if can i do a perl programme to do this ? because i have 195 sequences i can't repeat it 195. thank you

[Pierre Lindenbaum]

i ask if can i do a perl programme to do this

yes, you can, and we'll be happy to help you once you show us what you've started coding.

[GenoMax]

Better question to ask would have been "is it possible to write a local program (or is one readily available) to do what WEEDER is doing online"?

I assume perl part of the question is a red herring since if you were able to program in Perl you would not have asked this question in the first place.