[Bioperl-l] SimpleAlign and consensus_string

[Jason Stajich]

There are several methods that do related things. 

Below is the documentation for the method - it allows a more strict calling besides majority rule voting for the position - if you set the cutoff at 50% then the called AA or NT has to appear at least 50% of the time. There is also an IUPAC consensus string which is useful for DNA consensus generating patterns. 

If you want a summary as to whether or not there are only conservative amino acid changes in the column use match_line method which generates the similar string that CLUSTALW reports as a summary string for each column.

=head2 consensus_string

 Title     : consensus_string
 Usage     : $str = $ali->consensus_string($threshold_percent)
 Function  : Makes a strict consensus
 Returns   : Consensus string
 Argument  : Optional treshold ranging from 0 to 100.
             The consensus residue has to appear at least threshold %
             of the sequences at a given location, otherwise a '?'
             character will be placed at that location.
             (Default value = 0%)

=cut

On Dec 5, 2011, at 3:00 PM, Amin Momin wrote:

> Hi ,
> 
> I am generating a consensus sequence by aligning two protein homologs
> using Bio::Tools::Run::Alignment::TCoffee. However, I am unable to
> understand the criteria consensus_string() method of simpleAlign uses
> to determine the consensus at position with dissimilar aminoacids/
> nucleotide. Also how would the % cutoffs provided to
> consensus_string() affect the outcome.
> 
> 
> Thanks,
> Amin
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