[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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