I was just playing with the current jalview. The profile called "conservation looks odd". How has it been calculated? It should be the Zvelebil conservation values as are used for the colouring, but does not appear to be. Treatment of gaps is also odd. In the zvelebil system, a gap character is assigned all properties and so the conservation score is low at a gap, not high as is shown on the profiles.
I'd rather this profile was not shown on the example, until the above are fixed
Geoff
Funnily enough, I was just working on the alignment 'quality' meaure
that was in the old jalview because Andrew noticed that conservation!=quality
in the old program.
I'd rather this profile was not shown on the example, until the above are
fixed
Is the Zvelebil method described here ?
PREDICTION OF PROTEIN SECONDARY STRUCTURE AND ACTIVE-SITES USING THE ALIGNMENT OF HOMOLOGOUS SEQUENCES
ZVELEBIL MJ, BARTON GJ, TAYLOR WR, STERNBERG MJE
JOURNAL OF MOLECULAR BIOLOGY
195 (4): 957-961 JUN 20 1987
And do you have a copy of the paper anywhere ?
ta!
j.
On Thu, 7 Apr 2005 11:49:31 +0100 (GMT Daylight Time) Geoff Barton <geoff@compbio.dundee.ac.uk> wrote:
Funnily enough, I was just working on the alignment 'quality' meaure
that was in the old jalview because Andrew noticed that conservation!=quality
in the old program.
Aha, great minds and all that...
I'd rather this profile was not shown on the example, until the above are
fixedIs the Zvelebil method described here ?
PREDICTION OF PROTEIN SECONDARY STRUCTURE AND ACTIVE-SITES USING THE ALIGNMENT OF HOMOLOGOUS SEQUENCES
ZVELEBIL MJ, BARTON GJ, TAYLOR WR, STERNBERG MJE
JOURNAL OF MOLECULAR BIOLOGY
195 (4): 957-961 JUN 20 1987
Yes, and also in the amas paper (Livingstone and Barton) and Meth Enz review.
There is code to do the conservation calculation in C and java in Jalview (and fortran).
And do you have a copy of the paper anywhere ?
Probably, but I think the description of the calculation is better in the Livingstone and Barton papers. There is an on-line version on http://www.compbio.dundee.ac.uk/Publications/1993/1993.html ad also probably a pdf on:
http://www.compbio.dundee.ac.uk/ftp/preprints/
Geoff
On Thu, 7 Apr 2005, Jim Procter wrote:
On Thu, 7 Apr 2005 11:49:31 +0100 (GMT Daylight Time) > Geoff Barton <geoff@compbio.dundee.ac.uk> wrote:
------------------
Geoff Barton, Professor of Bioinformatics, School of Life Sciences
University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk
Tel:+44 1382 345860/345843 (Fax:345764) www.compbio.dundee.ac.uk