[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/1048

[Heikki Lehvaslaiho]

Jack,

The module containing the code for sequence patterns is written by Steve
Chervitz who is almost, but not quite as old, hand in bioinformatis as you.
8-)

Bioperlers,

The use of Z for hydrophilic does not seem to be a bug but a feature. The
logic of the module has not changed for long time. Maybe it is time to
reassess this module. Is anyone on the list using it and is the old usage of
B (hydrophobic aa) and Z (hydrophilic aa) symbols still useful? They are
certainly not commonly used in this meaning.

The SWISS-PROT database contains both B and Z symbols in sequences so one
should be able to use all UIPAC aa codes in pattern. On the other hand,
there are no PROSITE pattern using them, so I am not sure how real this need
is.

Opinions please,

	-Heikki

bioperl-bugs@bioperl.org wrote:
> 
> JitterBug notification
> 
> new message incoming/1048
> 
> Message summary for PR#1048
>         From: jackl@dalicon.com
>         Subject: Amino Acid "Z" incorrectly expanded
>         Date: Fri, 4 Jan 2002 07:27:49 -0500
>         0 replies       0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From jackl@dalicon.com Fri Jan  4 07:27:50 2002
> Received: from localhost (localhost [127.0.0.1])
>         by pw600a.bioperl.org (8.11.2/8.11.2) with ESMTP id g04CRnA19784
>         for <bioperl-bugs@pw600a.bioperl.org>; Fri, 4 Jan 2002 07:27:49 -0500
> Date: Fri, 4 Jan 2002 07:27:49 -0500
> Message-Id: <200201041227.g04CRnA19784@pw600a.bioperl.org>
> From: jackl@dalicon.com
> To: bioperl-bugs@bioperl.org
> Subject: Amino Acid "Z" incorrectly expanded
> 
> Full_Name: Jack Leunissen
> Module:  Bio::Tools::SeqPattern.pm
> Version: 0.7.2
> PerlVer: 5.6.1
> OS: Linux
> Submission from: dalicon.telebyte.nl (213.211.130.145)
> 
> In the example program "seq_pattern.pl" the first protein pattern contains the
> ambiguous amino acid "Z". Probably only old folks like myself know that this
> amino acid was used in old times to denote GLX, which is GLU or GLN
> (dansyl-Edman degradation used in protein sequencing was unable to discriminate
> between Glu and Gln, due to the acidic conditions used).
> However, the Bioperl module translates this amino acid incorrectly into
> "TSHEDQNKR"! Someone must be thinking that "Z" symbolises all polar amino acids,
> but this is wrong.It must defnitely be "EQ".
> 
> Regards,
> Jack
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________