New gene prediction E-mail server available

BORODOVSKY,MARK mb56 at prism.gatech.edu
Thu Apr 30 14:23:06 EST 1992


          GENMARK : SYSTEM FOR PREDICTING PROTEIN CODING REGIONS
                           Version 1.1  4/15/92
                    (Internet Electronic Mail Server)
 

GENERAL INFORMATION

     GenMark is a software package available from the Georgia Tech School of
Applied Biology  &  Office of Information Technology for the quick analysis of
newly sequenced DNA.

     GenMark 1.1 is based on a special type of Markov chain model of coding
and noncoding nucleotide sequences. It proves to be a quite sensitive indicator
of protein coding regions in E.Coli and closely related species. The yield of
false positive predictions from the analysis of a 96bp segment is about 10%, for
false negatives, about 22.5% . The process for training the program for other
species is fairly straightforward, and new species will be added later, based on
demand and available information. 

     GenMark is robust to the presence of ambiguities in newly sequenced DNA -
up to 10% of the sample DNA may be indicated by ambiguity symbols.

     GenMark receives its submissions from your local electronic mail service
and will reply with a list of open reading frames that it recognizes as protein
coding regions. There are also various other options, such as a PostScript(tm)
graph of the results, which may optionally be requested. GenMark should reply
within an hour of a sequence's submission by way of electronic mail.

     If you are interested in more detailed information on the system, please,
send an E-mail message to:

	genmark at ford.gatech.edu

with the word:

	instructions

in the subject line (the message body will be ignored). The detailed 
instructions will be sent to you shortly thereafter.







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