Heuristic Approach for Gene Prediction

Heuristic Approach for Gene Prediction

John Besemer and Mark Borodovsky
Heuristic approach to deriving models for gene finding
Nucleic Acids Research (1999) 27, pp 3911-3920

Wenhan Zhu, Alex Lomsadze and Mark Borodovsky
Ab initio gene identification in metagenomic sequences
Nucleic Acids Research (2010) 38, e132

This webpage provides accesses to heuristic gene finding parameters and to gene prediction program GeneMark.hmm prokaryotic (version 3.25).

Browse Heuristic Approach manual

Input sequence

Enter sequence (FASTA or multi FASTA format)

or, upload file:

Action

Options

Output format for gene prediction	Output options	Optional: results by E-mail
LST GFF	Protein sequence Gene nucleotide sequence Coding potential graph (not for multi FASTA) PDF PostScript	E-mail Subject Compress files

Advanced options

Select genetic code:
genetic code 11
"ATG" only start codon, genetic code 1
"TGA" codon as a Tryptophan (not as a stop codon), genetic code 4

Predict on strand:
both
direct
reverse

Heuristic parameters, as in 1999 publication
Heuristic (MetaGeneMark) parameters, as in 2010 publication