[Bioperl-l] Help on module for the analysis of sequence alignment

[Julio Fernández Banet]

Hello all!.

I would like to ask if there is a bioperl module that can extract 
information from an alignment obtained by bl2seq.
The kind of info I need to extract is the position of a change, the 
nucleotide in the two sequences and in case of a deletion or insertion 
the length and the sequence that was inserted/deleted.
The reason to do this is because I'm comparing the wild type sequence 
of my gene  of interest against the sequences obtained from my 
population of study and I would like to store this kind of information 
in a database to integrate genotype variation with phenotype

To be more descriptive I need something that works like this:


Alignment:
Seq1:  acgtacgtacgtacgt----acgt
              | | | | | | | | | |  |              | | | |
seq2:  acgtacgtacct----acgtacgt

Result from parsing:

Position 11 g  -> c
Position (13-16)insertion ACGT
Position (17-20)deletion ACGT

Thanks a lot.

Julio Fernández


PhD. Julio Fernández Banet
C/ Benito Corbal nº20 -6ºA
Pontevedra C.P. 36001
Spain

Phone: (0034)607747946
Web: http://www.freelancebio.com

PhD. Julio Fernández Banet
C/ Benito Corbal nº20 -6ºA
Pontevedra C.P. 36001
Spain

Phone: (0034)607747946
Web: http://www.freelancebio.com

PhD. Julio Fernández Banet
C/ Benito Corbal nº20 -6ºA
Pontevedra C.P. 36001
Spain

Phone: (0034)607747946
Web: http://www.freelancebio.com

PhD. Julio Fernández Banet
C/ Benito Corbal nº20 -6ºA
Pontevedra C.P. 36001
Spain

Phone: (0034)607747946
Web: http://www.freelancebio.com

PhD. Julio Fernández Banet
C/ Benito Corbal nº20 -6ºA
Pontevedra C.P. 36001
Spain

Phone: (0034)607747946
Web: http://www.freelancebio.com

PhD. Julio Fernández Banet
C/ Benito Corbal nº20 -6ºA
Pontevedra C.P. 36001
Spain

Phone: (0034)607747946
Web: http://www.freelancebio.com

PhD. Julio Fernández Banet
C/ Benito Corbal nº20 -6ºA
Pontevedra C.P. 36001
Spain

Phone: (0034)607747946
Web: http://www.freelancebio.com