[Bioperl-l] needs help...

Angshu Kar angshu96 at gmail.com
Thu Oct 13 19:28:14 EDT 2005

Hi ,

I need your help in solving a bioinformatics implementation problem.
 I'm stating my problem stepwise below:

1. There are amino acid sequences stored (clustered) in the database
(postgres) in raw format. e.g. Cluster A has 5 sequences, Cluster B has 3
and so on.
2. Each of those sequences (from one cluster at time, say, we pick the 5
sequences from Cluster A, one by one) needs to be picked up and converted to
fasta format.
3. These fasta files then need to be fed into a multiple sequence alignment
tool (e.g. CLUSTALW).
4. The tool needs to be executed and the results will be displayed.
5. The output of the tool (aligned sequences) then needs to be fed into a
scoring tool ( e.g. BLOSUM).
6. The scoring tool needs to be run and the scores need to be displayed in
histogram format (say Cluster A has score 5.5, Cluster B has score 3.3 and
so on).
 All these needs to be done using perl (or bioperl) and I'm completely new
to this. Could you please suggest me how to implement step 3-5?
 Thanking you,

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