GeneMarkS

Description

GeneMarkS is a gene prediction algorithm which utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic genome with no prior knowledge of any protein or rRNA genes [1].

More information at the GeneMark server [2].

Example output

GeneMark.hmm PROKARYOTIC (Version 2.1)
Sequence file name: sequence, RBS: Y
Model file name: GeneMarkS_plus_Heuristic_AT_and_NONC.mod
Model organism: Pseudonative.model
Wed Jan 12 19:08:39 2005

Predicted genes
   Gene    Strand    LeftEnd    RightEnd       Gene     Class
    #                                         Length
    1        +          <2         109          108        1
    2        -         160        1080          921        1
    3        +        1193        2527         1335        1
    4        -        2642        4390         1749        1
    5        -        4424        4519           96        1
    6        -        4554        5465          912        1
    7        +        5509        6264          756        1
    8        -        6394        8115         1722        1
    9        -        8116        8595          480        1
   10        +        8701        8829          129        1

References

1. Besemer J, Lomsadze A, and Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001 Jun 15;29(12):2607-18.
2. Besemer J and Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4. DOI:10.1093/nar/gki487 |