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UH Gene-Server Summary of Services

Dan Davison dbd at theory.uh.edu
Sat Nov 11 21:03:21 EST 1995

                The University of Houston Gene-Server
                         Services and Changes
                            November, 1995

1. Recently Added Services (MANY NEW SERVICES!)
2. The "Server Server" concept
3. Service Interruptions & Troubles
4. Addresses
   a. Gopher
   b. WWW
   c. FTP
   d. E-mail
   e. PIR Releases and Technical Notes
5. Some technical notes about servers
6. Acknowledgements

1. Recently added services

A. In collaboration with Dr. Victor Solovyev of the Computational Biology
Group, Baylor College of Medicine, we recently added a series of
servers for Drosophila. Arabhabopsis, and nematode gene identification.

dspl   - splice site prediction for Drosophila genes
fexd   - find exons in Drosophila genes
fgened - Drosophila gene modeling

aspl   - splice site prediction for Arabhadopsis genes
fexa   - find exons in Arabhadopsis genes
fgenea - Arabhadopsis gene modeling

nspl   - splice site prediction for nematode genes
fexn   - find exons in nematode genes
fgenen - nematode gene modeling

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 fexn

        service at bchs.uh.edu

b.  The Multiple Sequence Alignment Server 

We were recently funded by the National Library of Medicine to provide
a multiple sequence alignment service on the Internet.  ClustalV, MSA,
Treealign, and MAP are the programs available at


This server is derived in part from the BCM Sequence Launcher, by
Randy Smith of the Baylor College of Medicine in Houston.  The Search
Launcher is "one-stop shopping" for protein and nucleic acid analysis,
and is available at


Three more multiple sequence alignment algorithms are coming soon.  

We will also have email and client-server access in the coming months.
The email server will use the now-standard BLAST email server syntax.

2. The Server Server Concept        

As a part of our Internet services for molecular biologists, we are
also making the Gene-Server available as a "server server".  If you
have developed an analysis program and would like to make it available
on the net, but don't want to run a server yourself, you can arrange
for the Gene-Server to run it for you. Contact davison at uh.edu if you
would like more information.

3. Service Interruptions-New Building Construction

Due to circumstances well beyond our control, there have been a number
of network and power outages recently.  Since a building is being put
up next door, we will probably continue to have power interruptions.
We apologize for the inconvenience and will continue to work to
minimize the effects of power and network problems. If the budget
allows, we'll get some UPCs.

3. Addresses

   a. Gopher

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

   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 www.bchs.uh.edu. The URL is

   c. 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 

   d. 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 bchs.uh.edu
[Please note that is service is temporarily broken; look for it to be
replaced by service at bchs.uh.edu, described below)

2. DNA sequence characterization and protein secondary structure
prediction are available from

        service at bchs.uh.edu

Send the word "info" or "help" to that address to get started. The
previous address, "service at theory.bchs.uh.edu" will also work.

   f. PIR releases and Technical Notes

PIR releases are found on ftp.bchs.uh.edu in pub/gene-server/pir/pir_relXX, 
where XX is the release number (Current release is 46).  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,
          7.X, and 8.X program suite. 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 archive-server scripts from Brian Reid at
DECWRL, with extensive local modifications.  We also use 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), the National Library of
Medicine (LM 0575), and the Department of Energy Office of
Health and Environmental Research (DE-FG03-95ER62097/A000). 

dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77054-5934/davison at uh.edu/DAVISON at UHOU
"Christ, I'm an American, how can I fail to do good?" -Chris, in Miss Saigon
Disclaimer: As always, I speak only for myself, and, usually, only to

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