Eukaryotic GeneMark.hmm(1,2) (Reload this page)
References:
1Borodovsky M. and Lukashin A. (unpublished)
2Lomsadze A., Ter-Hovhannisyan V., Chernoff Y. and Borodovsky M.,
"Gene identification in novel eukaryotic genomes by self-training algorithm",
Nucleic Acids Research, 2005, Vol. 33, No. 20, 6494-6506
Accuracy comparison

Result of last submission:

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GeneMark.hmm Listing

Go to: GeneMark.hmm Protein Translations

Go to: GeneMark Listing

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GeneMark.hmm (Version 2.2a)
Sequence name: Tue Nov 22 13:31:16 EST 2011
Sequence length: 12239 bp
G+C content: 63.64%
Matrix: Homo sapiens
Tue Nov 22 13:31:16 2011

Predicted genes/exons

Gene Exon Strand Exon           Exon Range     Exon      Start/End
  #    #         Type                         Length       Frame
  1    10   -  Internal      1396      1459      64          3 3
  1     9   -  Internal      2392      2456      65          2 1
  1     8   -  Internal      3127      3252     126          3 1
  1     7   -  Internal      6455      6547      93          3 1
  1     6   -  Internal      6587      6736     150          3 1
  1     5   -  Internal      8837      8945     109          3 3
  1     4   -  Internal      9176      9220      45          2 3
  1     3   -  Internal      9696      9861     166          2 2
  1     2   -  Internal     10548     10737     190          1 1
  1     1   -  Internal     11113     11228     116          3 2

GeneMark.hmm Protein Translations

Go to: GeneMark.hmm Listing

Go to: GeneMark Listing

Go to: Job Submission


>Tue Nov 22 13:31:16 EST 2011_1|GeneMark.hmm|gene 1|374_aa
CEHVCGGLRVERVCTCVGACVWSVRARVWGPACGACVHGGTVIGSARCKAFTTREGRRAA
AYNLVQRGITNLCVIGGDGSLTGANIFRSEWGSLLEELVAEGKISESTARTYSHLNIAGL
VGSIDNDFCGTDMTIGTDSALHRIMEVIDAITTTAQSHQRTFVLEVMGRHCGYLALVSAL
ASGADWLFIPESPPEDGWENFMCERLGETRSRGSRLNIIIIAEGAIDRNGKPILSSYVKD
VRVGLGRPRGRHPARLGQLVVQRLGFDTRVTVLGHVQRGGTPSAFDRVLSSKMGMEAVMA
LLEATPDTPACVVSLSGNQSVRLPLMECVQMTKEVQKAMDDKRFDEAIQLRGRSFENNWN
IYKLLAHQKLSKEK

GeneMark Listing

Go to: GeneMark.hmm Listing

Go to: GeneMark.hmm Protein Translations

Go to: Job Submission



                              GENEMARK PREDICTIONS

Sequence: Tue Nov 22 13:31:16 EST 2011
Sequence file: gm_sequence
Sequence length: 12239
GC Content:  63.64%
Window length: 96
Window step: 12
Threshold value: 0.500
Matrix: human_62.mat
Matrix author: Nikolai Ivanov
Matrix order: 5

List of Regions of interest
(regions from stop to stop codon w/ a signal in between)

   LEnd      REnd    Strand      Frame
 --------  --------  ----------- -----
      123       452  complement  fr 2
      305       880  direct      fr 2
     1094      1669  complement  fr 1
     1282      1473  complement  fr 3
     1623      1934  complement  fr 2
     1847      2611  complement  fr 1
     2388      2561  complement  fr 2
     2986      3621  complement  fr 3
     3488      3904  complement  fr 1
     3624      4034  complement  fr 2
     6011      7120  complement  fr 1
     8687      9100  complement  fr 1
     9692     10093  complement  fr 1
    10234     11991  complement  fr 3
    10667     11932  direct      fr 2

List of Protein-Coding Exons
(regions between acceptor and donor site w/ coding function >0.500000)

  Left     Right
  End      End      Strand     Frame   Prob
 -------  -------  ----------- -----  ------
     324      400  complement   fr 2  0.6195
     336      379                     0.7173

     444      588  direct       fr 2  0.5444
     461      505                     0.7139

    1354     1464  complement   fr 3  0.6182

    1463     1624  complement   fr 1  0.5178
    1486     1619                     0.6082

    1524     1624  complement   fr 1  0.4823

    1526     1668  complement   fr 3  0.2942

    1634     1825  complement   fr 2  0.3791

    1634     1825  complement   fr 2  0.3791

    1893     2055  complement   fr 1  0.6093
    1959     2026                     0.9179

    2392     2467  complement   fr 2  0.8493
    2392     2446                     0.8013

    3125     3276  complement   fr 3  0.8187
    3125     3227                     0.8434

    3166     3276  complement   fr 3  0.8078
    3182     3227                     0.9453

    3527     3589  complement   fr 1  0.8417

    3757     3903  complement   fr 2  0.6273
    3765     3894                     0.6945

    3867     3903  complement   fr 2  0.4176
    3870     3894                     0.5067

    3965     4024  complement   fr 1  0.2622
    3981     4012                     0.2143

    4030     4089  complement   fr 3  0.2811
    4046     4077                     0.4583

    4527     4581  direct       fr 3  0.4962
    4541     4565                     0.5178

    6463     6753  complement   fr 1  0.6920
    6487     6743                     0.6794

    8812     9025  complement   fr 1  0.8005
    8840     9008                     0.9197

    9589     9693  complement   fr 2  0.3592
    9608     9681                     0.3864

    9601     9704  direct       fr 1  0.3993

    9701     9909  complement   fr 1  0.8221
    9731     9860                     0.9999

   10551    10735  complement   fr 3  0.9467
   10564    10727                     0.9941

   10877    10972  direct       fr 2  0.4679
   10926    10965                     0.5937

   11652    11737  complement   fr 2  0.2923
   11679    11737                     0.2564



ABOUT THE MATRIX USED:

Date: March 6, 2003
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