[Bioperl-l] clustalw output format

[Peter Schattner]

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