[Bio-Linux] Mult. sequence alignment editor program of interest forBio-Linux users?

[Nicolas Bertrand]

Really nice. Thank you!

Tried it on Windows and Linux.

Problems on Bio-Linux (and Windows):
pfaat could not find  hmmbuild (even so hmmbuild is in the path in
Linux, on windows hmmbuild was not even installed so no surprise, there
:-). Would be interesting to hear if somebody has got this working.

SRS Searching works. Should you want to query a different SRS server
(or change the database or field you need to search!), you have to edit
the file pfaat.properties in the pfaat installation directory 
the default line is:
pfaat.srsServer=srs.ebi.ac.uk/srs5bin/cgi-bin/wgetz?-e+[swall-id:QUERY_NAME]+-vn+2

I have changed it to point out to our internal SRS server as follows:
"pfaat.srsServer=ivgfs.nox.ac.uk/srs71bin/cgi-bin/wgetz?-e+[swall-id:QUERY_NAME]+-vn+2"
and could get some results back (See attachment). 

The tree viewing functionality  seems taken directly from  ATV,
software that is already included in Bio-Linux
:-)[http://www.genetics.wustl.edu/eddy/atv/]

Nic

**********************************************
Nicolas Bertrand   
IT Support, GRID & Bioinformatics
CEH Oxford, Mansfield Road
Oxford OX1 3SR
**********************************************


PS: I have to say though that pfaat feels significantly snappier on a
windows box than on Linux :-(

>>> "Bela Tiwari" <btiwari at ceh.ac.uk> 08/01/2004 14:44:39 >>>
Hello all,

I just finished reading about and trying out the program Pfaat, which 
is a graphical protein multiple sequence alignment program, but with
lots of bells and whistles.

Information about the program, and downloads can be found at:

http://pfaat.sourceforge.net/ 

Ripping info straight off their page:

"Key features of Pfaat include the ability to align collections of
sequences, cluster and/or group sequences into subfamilies, analyze
sequences based on a number of similarity criteria, visualize protein
structure, and annotate sequences and specific residue positions with
text descriptions. "

Dan and I just played around with it and were both quite impressed. We
are considering putting this onto a future release of Bio-Linux, and
if
any of you decide to give it a try, please let us know what you think
so
we know whether it is as useful to the user community as we think it
could be.

If anyone does try this out - we'd be interested to know if the SRS
functionality works for you or not. We ran the program on a machine
with
SRS already installed, so I'm not sure whether how they have
implemented
the SRS functions - local or via the web. (I know I could dig around
for
this and figure it out, but maybe one of you kind souls will let us
know
your experiences  should you try it.)


Installation:
All it took for me to install this on Bio-Linux was the following:

Make a directory for the installation and put the downloaded file into
this directory
Run the command:   sh install.exe            (or similar - check the
instructions for the program!)
Make a subdirectory from wherever you put the distribution called
"bin", then make a subdirectory under bin called "linux"
Inside that directory  (bin/linux), make softlinks to clustalw,
hmmbuild, hmmalign:

ln -s /usr/software/exec/clustalw   clustalw
ln -s /usr/software/exec/hmmbuild  hmmbuild
ln -s /usr/software/exec/hmmalign  hmmalign

I also set the environmental variable PFAAT to point to the directrory
where the distribution was. (I put this in my home directory .zshrc
file, but if you wanted it to be universally applicable, you could put
it in /usr/software/bioenvrc, or into /etc/zshrc...or whatever the
appropriate global file is for the default shell on your machine if
you
have changed it.)

As I recall, that's all I did.

They have an example directory where you can load up an alignment,
etc.


Please let us know if you try this program and what you think. We're
also always happy to hear about software you discover out there that
looks like it might be of interest to other Bio-Linux users.


cheers

Bela


*************************
Dr. Bela Tiwari
Lead Bioinformatician

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************





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