[Bioperl-l] AlignIO::clustalw match_line query

[Jason Stajich]

Implemented independently, but it was based on what the clustalw  
documentation says.
The main code is in the match_line function in Bio::SimpleAlign.

See the CONSERVATION_GROUPS Hash which looks like this: So a  
'strong' (":") on the match line would be coded where the residues  
seen in a column are only 'S', 'T', or 'A' (for example).

            'strong' => [ qw(
				STA
				NEQK
				NHQK
				NDEQ
				QHRK
				MILV
				MILF
				HY
				FYW )],
             'weak' => [ qw(
				CSA
				ATV
				SAG
				STNK
				STPA
				SGND
				SNDEQK
				NDEQHK
				NEQHRK
				FVLIM
				HFY )],);
}

It was checked against clustalw output by hand when it was  
implemented. If you know of any inconsistencies, let use know.

-jason
On Aug 6, 2008, at 6:11 PM, Richard Francis wrote:

> Dear List,
>
> I wonder if you can help.
>
> I’m having trouble finding out on which criteria the conserved and
> semi-conserved substitution decisions for a match line produced  
> from the
> match_line function in AlignIO are based.
>
> I note that match_line produces the same output as an alignment match
> line would from ClustalW and indeed is used in the AlignIO::clustalw
> module, but are the substitution decisions based on the same Venn
> diagram at http://www.ebi.ac.uk/Tools/clustalw2/ 
> clustalw_help.html#color
> ie are they faithful to the generation of the match line from within
> ClustalW itself?
>
> I need to know this as part of a paper I’m writing so I would really
> appreciate your help with this.
>
> Kind regards and thanks in advance,
>
> Richard Francis
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