[Bioperl-l] clustalw output format
Mon, 15 Oct 2001 16:04:28 -0700
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.
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.