[Bioperl-l] SimpleAlign and consensus_string

[Amin Momin]

Thanks Jason


On Mon, Dec 5, 2011 at 5:58 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> 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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>