[Bioc-devel] MSA Consensus

[Ulrich Bodenhofer]

Hi Natalie,

Sorry, there is presently no such function in the 'msa' package and, as 
far as I know, there is no such thing in 'Biostrings' either. If you can 
specify us an exact formula how to compute the score you are 
particularly interested in (or at least point us to a reference), we can 
try to implement it before the next major release in April. Note that 
the msaPrettyPrint() function is just a wrapper around the LaTeX package 
'texshade'. No matter what 'texshade' may do internally, we have no 
access to its internal functionality from R.

Thanks and best regards,
Ulrich

> Date: Mon, 13 Mar 2017 17:36:22 +0000
> From: Natalie Stephenson <N.L.Stephenson at leeds.ac.uk>
> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: [Bioc-devel] MSA Consensus
> Message-ID:
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>
> Hi,
>
> I was wondering if you would be able to tell me whether it is possible to get the calculated conservation score (GONNET PAM250 matrix) from an alignment produced by MSA?
> >From what I understand from your literature, this is something that is calculated in msa by ClustalW, as it is possible to specify an arbitrary (. : !) identifier based on this score when performing msaPrettyPrint(). However, I would prefer to specify an output that gave consensus sequence with a numeric PAM conservation score for each residue position in the alignment. Is this something that I can get from the msa tool?
>
> Thanks for your advice of this matter.
>
> Best wishes,
> Natalie