[Bioperl-l] Multiple sequence alignment consensus generation

[Heikki Lehvaslaiho]

BioPerlers,

David and I have been working together to get a IUPAC consensus atring out
of SimpleAlign. I think everything one might expect of this method is now in
place in bioperl-live.

Try consensus_iupac() on RNA or DNA alignments. Moltype, gaps and even
ambuigity codes within alignment have been taken into account. 

Note on performance: the implemented if/else structure and rexeps on a
string is >50 faster than using a hash or an array to store regexps.

	-Heikki



Heikki Lehvaslaiho wrote:
> 
> David,
> 
> UnivAlign is not supported any more. I've been adding more methods into
> SimpleAlign lately but have not thought about doing this and doubt anyone
> has the code ready. It should be easy  enough to do by modifying a copy of
> the  existing consensus code. Do you want to do it? I'd be happy to put into
> the distribution file.
> 
>         -Heikki
> 
> "David J. Evans" wrote:
> >
> > I'm working on a project in which I need to generate single letter codes for
> > non-conserved positions in an alignment i.e Y = C or T, B = C or G or T.
> > I'm, using UnivAln and/or SimpleAlign to handle my alignments - both will
> > generate consensuses (consensi ?), but of the format ACGGG!!T as opposed to
> > ACGGGYBT.  Has anyone written a subroutine to achieve this, and if not,
> > would others find it useful ?  If the former, could it be posted ?
> > David
> >
> > =====
> > David J. Evans
> > Institute of Virology  |  David.Evans@vir.gla.ac.uk
> > University of Glasgow  |  Tel/Fax : +44 0141 330 6249
> > Church Street          |  SMS/Mobile : +44 07940 592768
> > GLASGOW G11 5JR        |  http://www.polio.vir.gla.ac.uk/
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________