[Biopython-dev] Server request

Iddo Friedberg idoerg at cc.huji.ac.il
Mon Dec 3 05:22:20 EST 2001

Hi all,

I am not sure to whom this request should be addressed, but as this may be
of general interest to most people on the list, I am putting it here.

I have recently completed the first stage of what I call the PeCoP
("pea-cop") server. Briefly, the user enters a sequence, and receives an
annotated output of conserved positions, as determined by multiple
PSI-BLAST runs. Due to some recent manpower reshuffle, my faculty is
not-that-equipped to handle mounting of CGI-script driven pages. So I'm
bumming around. Any chance of getting this hosted on biopython.org?

As PeCoP drives a modified version of standalone PSI-BLAST,
it needs the following:

1) An installed standalone version of "my" PSI-BLAST (blastpgpI). Probably
my binary, compiled on  Linux  2.2.16-22 will work. If not, I can always

2) The biggie: NCBI datbase versions of sequence databases. Currently I
use nrgb, whose size is in the 390MB region. Actually, that's an old nrgb.
The latest version is probably a bit larger.

For now, biopython is used in a very rudimentary fashion in PeCoP. Parsing
fasta format, mainly. But the use of it will grow as I add features...




Iddo Friedberg                                  | Tel: +972-2-6757374
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |

More information about the Biopython-dev mailing list