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John Besemer john at amber.biology.gatech.edu
Fri Jun 12 09:29:09 EST 1998

To Chlamydomonas Researchers,

Thank you for your interest in using GeneMark.hmm.

The Chlamydomonas version is now online. It can be accessed at:

A few notes on using GeneMark.hmm:

1.  The maximum length for predicted exons is 3000 bases. If your sequence
contains exons longer than this, they will most likely be represented as
exons near 3000 bases in size with very small introns separating them.

2.  The maximum length for predicted introns is 1319 nucleotides.

3.  The shortest a predicted intron can be is 57 nucleotides.  The
shortest possible predicted exon is 3 nts.

These issues will cease to be problems when the database is more
representative of the actual exon and intron length limits in

If you require any assistance, feel free to email me:
john at amber.biology.gatech.edu

Thanks and happy gene finding,
John Besemer
Dr. Borodovsky's Bioinformatics
Lab Georgia Institute of Technology

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