[BiO BB] clustalw alignment pairwise

Daniele Santoni Daniele.Santoni at caspur.it
Fri Jul 28 07:38:45 EDT 2006


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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