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The Prokaryotic GeneMark.hmm Output
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gmhmmp
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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
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LeftEnd
|
RightEnd
|
Gene
|
Class
|
|
#
|
|
|
|
Length
|
|
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1
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+
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<3
|
98
|
96
|
2
|
|
2
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+
|
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
|
-
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6529
|
7911
|
1383
|
1
|
|
8
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+
|
8238
|
9191
|
954
|
1
|
|
9
|
+
|
9306
|
9893
|
588
|
1
|
|
10
|
-
|
9928
|
10494
|
567
|
1
|
|
11
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-
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10643
|
11356
|
714
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1
|
|
12
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-
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11382
|
11786
|
405
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1
|
|
13
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+
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12163
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14079
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1917
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1
|
|
14
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+
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14168
|
15298
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1131
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1
|
|
15
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+
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15445
|
16557
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1113
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2
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