What's the use of GeneMark-ES software?

This article mainly introduces the use of GeneMark-ES software, the article is very detailed, has a certain reference value, interested friends must read it!

GeneMark-ES software is used to predict protein-coding genes in eukaryotes. unlike other software to predict gene structure, it uses unsupervised algorithms and can be predicted independently of training sets. The official website is as follows

Http://exon.biology.gatech.edu/GeneMark/gmes_instructions.html

The installation process is as follows:

Wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_lqacT/gm_key_64.gzwget http://topaz.gatech.edu/GeneMark/tmp/GMtool_lqacT/gm_et_linux_64.tar.gztar xzvf gm_et_linux_64.tar.gzgunzip gm_key_64.gzcp.. /.. / gm_key_64 ~ / .gm_key

The gm_key file is the pass of the software, which needs to be copied to the home directory, and the software itself only needs to be unzipped.

The basic usage is as follows

Gmes_petap.pl-ES-cores 10--sequence genome.fa

Gmes_petap.pl itself integrates the functions of geneMark-ES and geneMark-ET. Genemark-ES is used for genomic data prediction and geneMark-ET is used for transcriptome data prediction.

-- ES indicates that the genemark-ES algorithm is used,-- cores specifies the number of parallel CPU,-- sequence specifies the input sequence in fasta format.

For fungi, there are special parameters. Examples are as follows

Gmes_petap.pl-fungus-cores 10--sequence genome.fa

In the default configuration, the output file is named genemark.gtf, which is saved in the installation directory of the software, and the structural information of the gene is recorded in GTF format.

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