Gmove

Dependencies

The script is written in c++, it uses the library boost (http://www.boost.org/) You should install them and change the path in the Makefile, before compiling it.

Running Gmove

gmove -f <reference sequence> --rna <rna.gff> {Options}

Option

gmove - Gene modelling using various evidence.

Arguments with * are required, the other are optionnal !!

 INPUT FILES
        *-f <file>              : fasta file which contains genome sequence(s).
        --rna <file>            : rna file in gff (expect tag 'exon' or 'HSP' in column 3)
        --prot <file>           : prot file in gff (expect tag 'exon' or 'HSP' in column 3)
        --annot <file>          : annotation file in gff (expect tag 'CDS' or 'UTR' in column 3)
        --abinitio <file>       : ab initio file in gff (expect tag 'CDS' or 'UTR' in column 3)

 OUTPUT FILES
        -o <folder>             : output folder, by default ./out
        --raw                   : output raw data

        --ratio                 : ratio CDS/UTR min 80% de CDS
        -S                      : do not output single exon models.
        -e <int>                : minimal size of exons, default is 9 nucleotides.
        -i <int>                : minimal size of introns, default is 9 nucleotides.
        -m <int>                : maximal size of introns, default is 50.000 nucleotides.
        -p <int>                : maximal number of paths inside a connected component, default is 10,000.
        -x <int>                : size of regions where to find splice site around covtigs boundaries, default is 0.
        -b <int>                : number of nucleotides around exons boundaries where to find start and stop codons, default is 30.
        -t                      : gtf format annotation file - default is gff3
        --cds                   : min size CDS, by default 100
        -h                      : this help`

Input

Gmove reads GFF2 and GFF3 files. It recognizes some specific tags at column 3 :

• for files parse with the options --rna and --prot, it recognizes the tags HSP and exon
• for files parse with the option --annot and --abinitio, it recognizes the tags UTR and CDS

Preparing the files

The transcript/protein's id (in the last column of the GFF files ) has to be uniq.

You should sort your files : the exon with the smaller position on the genome should be at the first line of the transcript. In this way Gmove can reconstruct the transcript/protein by just reading once the files. So be careful, when the strand is "-", Gmove needs to read the last exon first for a corresponding transcript/protein. 

Output

The script will output a GFF or GTF file. If the --rawoption is used, all of models will be output in a folder raw/. The selected models are output in a folder filter/

Installation

Install the dependencies

Download the git repository

Change the path to the dependencies in the Makefile

make gmove

License

Gmove is distributed open-source under CeCILL FREE SOFTWARE LICENSE. Check out http://www.cecill.info/ for more information about the contents of this license.

Contact

gmove [a] genoscope [.] cns [.] fr

Acknowledgments

This work was financially supported by the Genoscope, Institut de Genomique, CEA and Agence Nationale de la Recherche (ANR), and France Génomique (ANR-10-INBS-09-08).