GeneMark.hmm Manual
(prokaryotic)





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The Prokaryotic GeneMark.hmm Output gmhmmp

Interpreting the Prokaryotic GeneMark.hmm Output

GeneMark.hmm output contains predicted protein-coding genes.   The output will be a file divided into three sections as follows:

The Output Header

Each output generated by GeneMark.hmm has a header describing the parameters and matrix used in the analysis. This information is purely for recordkeeping purposes. Here's a sample header:

GeneMark.hmm PROKARYOTIC (Version 2.1)
Sequence file name: U00096.fna, RBS: Y
Model file name: e.coli2rbs.mod
Model organism: E.coli
Mon Jun 23 11:41:51 2003

The Predicted Gene Boundaries

This section describes the predicted genes.The ' Gene #' column is the sequential gene number. ' Strand ' indicates which strand the gene was found on -- ' + ' refers to direct, ' -' to complementary.' LeftEnd/RightEnd ' indicates the codon positions of the gene boundaries.' Gene Length ' indicates the length of the predicted gene.' Class' indicates the model which was used to predict the gene (for duel-model model files)

Predicted genes
Gene Strand LeftEnd RightEnd Gene Class
#       Length  
1 + <3 98 96 2
2 + 337 2799 2463 1
3 + 2801 3733 933 1
4 + 3734 5020 1287 1
5 + 5243 5530 288 1
6 - 5683 6459 777 1
7 - 6529 7911 1383 1
8 + 8238 9191 954 1
9 + 9306 9893 588 1
10 - 9928 10494 567 1
11 - 10643 11356 714 1
12 - 11382 11786 405 1
13 + 12163 14079 1917 1
14 + 14168 15298 1131 1
15 + 15445 16557 1113 2

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