Summary of UH Gene-Server Services

Dan Davison dbd at theory.BCHS.UH.EDU
Mon Nov 14 14:54:58 EST 1994

                The University of Houston Gene-Server
                         Services and Changes
                            November, 1994

1. Recently Added Services
2. Services to be removed
3. Service Interruptions
4. Addresses
   a. Gopher
   b. WWW
   c. WAIS
   d. FTP
   e. E-mail
   f. PIR Releases and Technical Notes
5. Some technical notes about servers
6. Acknowledgements

1. Recently added services

In collaboration with Dr. Victor Solovyev of the Computational Biology
Group, Baylor College of Medicine, we recently added a series of
servers for human gene identification and protein secondary structure

hexon  - find coding regions 
hspl   - splice site prediction for human genes
fexh   - find exons in human genes
fgeneh - human gene modeling
ssp    - protein secondary structure protein
nnssp  - neural net-based protein secondary structure prediction

Full details of each of these have been posted separately.  You can
obtain help files by sending the subject line
        man <servicename>
such as
        Subject: man hexon

        service at
2. Services to be removed

Due to better services being available elsewhere, the UH Gene-Server
will discontinue providing GenBank entries on November 30, 1994.  Users
requesting GenBank entries after that date will receive a note
referring them to the RETRIEVE server at

PIR and software retrieval by e-mail will NOT be affected by this

3. Service Interruptions

Due to circumstances beyond our control, there have been a number of
network and power outages recently.  We apologize for the
inconvenience and will continue to work to minimize the effects of
power and network problems.

4. Addresses

   a. Gopher

The UH Gene-Server Gopher service is available at;
it contains PIR sequence retrieval pointers to other Bio-Gophers, and
some local information. The URL is gopher://

   b. WWW

The Web pages offering access to the FTP site, descriptions of
software, a yellow pages of molecular biology software, and more.
Point your WWW browser at The URL is

   c. WAIS

WAIS indexed software descriptions are most easily accessed by using a
Web or Gopher client to or,

   d. FTP

The Gene-Server anonymous FTP area offers PIR releases, Mac, DOS,
Unix, and VMS molecular biology software, and more. It can be accessed
by anonymous FTP'ing to

   e. E-mail services

1. Users with access to electronic mail may retrieve molecular biology
software and data from the Gene-Server.   To start, send the word
"HELP" in the subject line or in the body of the message to 
        gene-server at

2. Human DNA sequence characterization and Protein secondary structure
prediction are available from
        server at
Send the word "info" or "help" to that address to get started.

   f. PIR releases and Technical Notes

PIR releases are found on in
where XX is the release number (Current release is 42).  There are
three directories:

ascii - the ascii version of PIR as released by NBRF. Compressed with
        Unix compress.
vms   - the "converted' VMS version of PIR, for use with the GCG 6.X and
        7.X  program suite (I'm not sure about 8.0 - we can't run
        Solaris and can't check). Compressed with Unix compress.
vms_lzw - the VMS version of PIR that retains VMS RMS (file)
          attributes, for NBRF's sequence analysis and handling
          system. Compressed with LZCOMP.

VMS executables of LZCOMP and LZDCOMP are in pub/gene-server/pir.
Version-specific files and release notes are available in
...pir/pir_relXX, as described above.

        PIR Technical Notes, which are important to check if you write
software to parse PIR format, are in pub/gene-server/pir/pir_tech.
The most recent note is PIRTECH06.LIS.

5. Some technical notes about servers

Important note: nnssp, the neural net secondary structure prediction
program, takes a lot of CPU time on my workstation, so it runs at a
very low priority. 

No more than two analysis routines may run at one time due to CPU

The Gene-Server uses the archive-server scripts from Brian Reid at
DECWRL, with extensive modifications.  The service at address
uses the Enterprise Integration Technologies ServiceMail Toolkit,
written in Ousterhout's Tool Command Language (Tcl).  

6. Acknowledgements

The Gene-Server project was started by Jack Chappelear and Dan
Davison, with assistance from Edward Chen, Bob Rimkus, and Manish
Doshi.  The various incarnations of the Gene-Server have been
supported by the University of Houston VP for Information Technology,
the UH Institute for Molecular Biology, and the National Science
Foundation (BIR-91-91165 and BIR 94-03562). 

Questions about the Gene-Server can be directed to Dan Davison, 
davison at  Questions about specific analysis services should
be directed to the address given in the help file for that service.

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