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  • how to create mat file for genemark

    I have genemarks.pl, makemat, viewamt, gmhmm in my path.
    After running, genemarkS, I get .mod and .mat file for model and matrix of that genome respectively.

    I can use these file for genemark and genemark.hmm for further gene prediction.
    But if I do not want to use genemarkS, how do I get the .mod & .mat correctly?

    I went through read me file and says to use probuild and mkmat
    mkmat [-x] <coding file> <noncoding file> <order> <output file>
    I do not have coding and noncoding file of the genome.

    ~/bin/genemark/gmsuite/probuild par -par_1.default -mkmod mod nz.fna
    where nz.fna is fasta file of genome
    mod is the model output name.

    I have par_1.deault in my folder where genome file is present, when I try to run the above command, I get error as:

    error in command line
    Bioinformaticscally calm

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