IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

BLOCKS searches on VAX/VMS and Alpha/OpenVMS

Thu Jan 28 08:19:43 EST 1993

In <Fuchs-270193150431 at rainer-mac.embl-heidelberg.de> Fuchs at EMBL-Heidelberg.DE writes:

> A new program, BlockSearch, is available for the analysis of new protein
> sequences using site-specific scoring matrices derived from Steven and
> Jorja Henikoff's BLOCKS database. The program was developed primarily for
> VMS/OpenVMS systems, but is written in ANSI C and should work on other
> platforms as well. It reads sequences in a variety of formats, including
> SWISS-PROT and GCG. A comparison of a typical-length protein sequence
> against BLOCKS release 6 takes about 15-20 CPU secs.
> A copy can be obtained from ftp.embl-heidelberg.de
> (/pub/software/vax/blksrch.uue) or by email from netserv at embl-heidelberg.de
> (get vax_software:blksrch.uue).
> Rainer Fuchs
> EMBL Data Library
> Fuchs at EMBL-Heidelberg.DE

I had a small problem with the frequency tables provided with the program 
source: Blocksearch complains about their format. Just edit the files
and remove the  blank line between the comments (lines beggining with '#')
and the table itself.

I wrote a small DCL script that perhaps helps using the program. It can be
fetched by anonymous ftp from biomed.uio.no ( Look in the
root directory for a DCL file called RUN_BLOCKS.COM. Edit the file to
customize it to your local setup. There is the command 'Fetch' which should
be removed for sites that don't have GCG.


                             Rodrigo Lopez
          * Work:       The Norwegian EMBnet node            *
          *             The Biotechnology Centre of Oslo     *
          * Address:    Gaustadalleen 21, N-0371 Oslo Norway *
          * Telephone:  +47-2-958756                         *
          * Fax:        +47-2-694130                         *
          * Electronic mail addresses (Internet)             *
          * rodrigol at ulrik.uio.no      UNIX                  *
          * rodrigol at biomed.uio.no     VMS                   *

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