ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER

Jeroen Coppieters jecop at ebi.ac.uk
Thu Jun 22 08:33:53 EST 1995


ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER

>From June 20th on, GeneMark will be reachable at the 
EMBL Outstation - The European Bioinformatics Institute (EBI), Hinxton, UK

EMAIL:       genemark at embl-ebi.ac.uk  (or genemark at ebi.ac.uk)

as well as on the original site 
School of Biology, Georgia Institute of Technology (Atlanta, GA)

EMAIL:      genemark at ford.gatech.edu

Since its first announcement, the GeneMark program has undergone continuous 
improvements, and more species matrices are made available for usage with
the service. The EMBL-EBI server is a mirror of the Georgia one, and thus will
return the same results for the same queries.

1.    SHORT OVERVIEW OF GENEMARK FEATURES
---------------------------------------------
The GeneMark server provides e-mail based identification of protein coding
regions in DNA sequences from prokaryotic and eukaryotic species. The GeneMark
server accepts a formatted message containing a DNA sequence in text format.
You may specify a species name, and parameters that control the analysis
procedure.

The current GeneMark version is accurate for finding prokaryotic genes and for
analyzing cDNA sequences to discriminate coding regions from non-coding ones
like 5' or 3' UTRs.

This program is able to identify rather long exons (more than 100bp) in
eukaryotic genomic DNA. This information can be used for designing RT-PCR or
PCR primers.
        
The GeneMark gene identification program has been developed at
the School of Biology, Georgia Institute of Technology (Atlanta, GA).

More details on the algorithm can be found in the paper:
Borodovsky M. and McIninch J.D.,
GeneMark: Parallel gene recognition for both DNA strands,
Computers & Chemistry, 1993, 17, 123-133.


2.   SENDING DATA TO GENEMARK
-----------------------------------------------------

A DNA sequence should be sent via e-mail to one of the following addresses:

        genemark at ford.gatech.edu
or
        genemark at embl-ebi.ac.uk


... with the word 'genemark' in the 'Subject:' field 
There is only one mandatory keyword:
DATA
 which must precede the text of the DNA sequence.

Below is given a simple example of sending a sequence to the GeneMark server
from a UNIX-based computer (note, that the '%' symbol is the prompt used
by the system, and that lower-case letters in the sequence text, numbers and
spaces are also acceptable): 

% mail genemark at embl-ebi.ac.uk        (or  % mail genemark at ford.gatech.edu)
Subject: genemark
data
TCCAGCTACTGCTGCTAGCTACGCTAGTCG........

%

When the server receives such a message, with almost no special options
indicated, it will analyze the sequence using default options and send
back a minimal response. Namely, it will use E. coli based parameters (by
default) and send back to the submitter a message containing a list of
those open reading frames that have been assessed as protein coding regions. 

You may, however, wish to get more information from the server. In that
case, please retrieve the HELP-Message from the GeneMark server,
which contains a full description of all commands and options


3.   GETTING THE HELP MESSAGE FROM GENEMARK
------------------------------------------------
Send an e-mail with the word HELP in the 'Subject:' field to

        genemark at ford.gatech.edu
or
        genemark at embl-ebi.ac.uk


4.    THE LIST OF SPECIES THAT CAN BE ANALYZED USING GENEMARK
------------------------------------------------------------------------------
NOTE: The EMBL-EBI server supports retrieval of the current list of
      supported species. Send a message to genemark at embl-ebi.ac.uk
      with the command LIST ORG in the SUBJECT

The matrix is specified using the 'SPECIES' command 

Use the line 
 'species <matrix>'
anywhere before the line
'data'
 where <matrix> is the name of one of the matrices listed below:

Matrix Name     Species
-----------     --------------------------------------------------------------
arab            Arabidopsis thaliana
capri           Mycoplasma capricolum (TGA = Trp)
celegans        Caenorhabditis elegans
chicken         Gallus gallus
disco           Dictyostelium discoideum
ecoli           Escherichia coli "native" genes [DEFAULT]
ecophage        Escherichia coli horizontally transferred genes
euglena         Euglena gracilis
eugchlor        Euglena gracilis chloroplasts
frog            Xenopus laevis
fruitfly        Drosophila melanogaster
human           Homo sapiens
kpneu           Klebsiella pneumoniae
lacto           Lactococcus species 
leprae          Mycobacterium leprae
mouse           Mus musculus
plasm           Plasmodium falciparum
rat             Rattus norvegicus
salm            Salmonella typhimurium
spombe          Schizosaccharomyces pombe
subt            Bacillus subtilis
tuberc          Mycobacterium tuberculosis
t4              Phage T4
urchin          Lytechinus pictus
yeast           Saccharomyces cerevisiae
--------------------------------------------------------------------------



--
==============================================================
         . O .                               Jeroen Coppieters
     . O O o   O .                            Software Support
   O O O O *o    O O          Jeroen.Coppieters at embl-ebi.ac.uk
  O O O O(   *o  )O O                     (or jecop at ebi.ac.uk)
  )O O O O   o*  O O(                         ++44 1223 494422 
  O O O O( o*    )O O
  )O O O O  *o   O O(                      EMBL Outstation EBI
  O O O O(   *o  )O O      (European Bioinformatics Institute)
  )O @ O O   o*  O O(                             Hinxton Hall
    O O O( o*   )O('                                   Hinxton
     ` O(   *o O  '                         Cambridge CB10 1RQ
         ` O '                                              UK
http://www.ebi.ac.uk
==============================================================



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