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

[Heikki Lehvaslaiho]

Julio,

We do not have anything ready that would do it, but it should not be too 
difficult it.

We have:

Bio::AlignIO::bl2seq, that can allows Bio::AlignIO to read bl2seq output
Bio::SimpleAlign,     is the structure that stores the alignment
                      it has a lot of methods
Bio::Variation::SeqDiff
Bio::Variation::DNAMutation
                      for storing the variation information

also,
Bio::Coordinate::Utils->from_align($aln)
                      that can be used to calculate sequence positions


Using these, it should be possible to do what you need.

Part of the problem is task specific and is best done in a script but some of 
it could be put in a utility method into BioPerl:
- take an alignment as the first argument
- assume that first seq is the reference,
  allow to change that using second argument
- to simplify things, allow only pairwise alignments
- process the alignment and return a Bio::Variation::SeqDiff object holding 
all detected Bio::Variation::DNA::Mutations


The script would take care of reading in the alignment and processing the 
output for printing or for adding into the database.


Is this something you could write and give the method back to be included into 
BioPerl?

Yours,
 -Heikki

P.S. You do know of the EMBOSS program diffseq, don't you?
     http://emboss.sourceforge.net/apps/diffseq.html



On Thursday 30 June 2005 01:26, Julio Fernández Banet wrote:
> 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________