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Old 04-30-2010, 03:48 AM   #1
torbean
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Location: EMEA

Join Date: Feb 2009
Posts: 11
Lightbulb GeneMark: gene finding. How does it work?

Hi all

There is a package of soft for gene prediction in sequences. Quite nice and used in some papers.

http://exon.gatech.edu/GeneMark/
http://exon.gatech.edu/GeneMark/metagenome/index.cgi

Though, there is no good manual for the software on web-pages (or I can't find them).

My questions to those who are familiar are the following:

1. Is is possible to analyse fasta file with multiple entries? If yes, how? Like special requirements for FASTA-format etc.

2. How can GeneMark take a seq of ~60 bases and "predict" me numerous (50) genes of ~200 bases?

3. Generally, is it trustworthy? Did you work with it enough to feel it was fine?

Sorry, questions are very general, but I am new to this soft, got a bit (well, a lot) puzzled today.
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