[Bioperl-l] clustalw output format
Jason Eric Stajich
Mon, 15 Oct 2001 19:49:08 -0400 (EDT)
Thanks Peter - will work on implementing this - I guess I should have
perused the manual more carefully.
On Mon, 15 Oct 2001, Peter Schattner wrote:
> Jason Eric Stajich wrote:
> > In a Clustal alignment what do the '.' and ':' signify - I assume
> > conservative transitions either by hydrophobicity and charge or from
> > BLOSUM matrices, not sure how I would calculate them though without
> > knowin exactly what they code for.
> > I
> Here's an except from the clustalw documentation that should help:
> 12.The conservation line output in the clustal format alignment file has
> been changed. Three characters are now used: '*' indicates positions which
> a single, fully conserved residue ':' indicates that one of the
> following 'strong' groups is fully conserved:-
> '.' indicates that one of the following 'weaker' groups is fully
> These are all the positively scoring groups that occur in the Gonnet
> Pam250 matrix. The strong and weak groups are defined as strong score >0.5
> and weak score =<0.5 respectively.
> - Peter