[Bioperl-l] clustalw output format

[Jason Eric Stajich]

Thanks Peter - will work on implementing this - I guess I should have
perused the manual more carefully.

-jason

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
> have
>        a single, fully conserved residue ':' indicates that one of the
> following 'strong' groups is fully conserved:-
>
>                         STA
>                         NEQK
>                         NHQK
>                         NDEQ
>                         QHRK
>                         MILV
>                         MILF
>                         HY
>                         FYW
>
>        '.' indicates that one of the following 'weaker' groups is fully
> conserved:-
>
>                         CSA
>                         ATV
>                         SAG
>                         STNK
>                         STPA
>                         SGND
>                         SNDEQK
>                         NDEQHK
>                         NEQHRK
>                         FVLIM
>                         HFY
>
>        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
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu