Perl programming sequence
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
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Pierre Lindenbaum
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titoo •
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what is the question ?
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
yes, you can, and we'll be happy to help you once you show us what you've started coding.
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
perlpart 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.