[BiO BB] clustalw alignment pairwise

[Paulo Nuin]

Hi

Isn't one of your first objectives to identify deletions? It seems that you
have found one. Most of the alignment looks pretty good to me. What you
might try is to use another program and compare the results.

HTH

Paulo


-----Original Message-----
From: bio_bulletin_board-bounces+pnuin=terra.com.br at bioinformatics.org
[mailto:bio_bulletin_board-bounces+pnuin=terra.com.br at bioinformatics.org] On
Behalf Of Daniele Santoni
Sent: July 28, 2006 7:39 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] clustalw alignment pairwise

Hi everybody, 

We are aligning a sample sequence with a consensus sequence in order to 
identify mutations, deletions and insertions.
Due to the presence of gaps we lack the correct open reading frame as you 
can see below (seqA). Can we solve the problem using some options of 
clustalw? 

This is an example:
cons   TTAACCCCACTCTGTGTTACTTTAAATTGCACTGATTTGATGAATGCTACTAATACCAAT 60
seqA   TTAACCCCACTCTGTGTTACTTTAAATTGTAATGGCACTCGAAACAGCACTCAAAACAGC 60
       ***************************** * **        **    *** * * ** 

cons   ACTACTATAATATATAGATGGAGAGGAGAAATAAAAAACTGCTCTTTCAATATCACCACA 120
seqA   ACC-CTGGAA-----GAAAAGTCAGGGACAATACAAAACTGTTCTTTCAATATGACCACA 114
       **  **  **       *  *  ***   **** ******* *********** ****** 

Thank you in advance for every suggestions 

Best regards 

Daniele
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