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
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--
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. 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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