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  • bio_informatics
    Senior Member
    • Nov 2013
    • 182

    how to select between genemark.hmm and genemarkS

    Dear Group Members,
    I am working on prokaryotic genome to predict genes. Neisseria meningitidis organism.
    Input file is multi contig fasta format.

    output gff3 file format is needed.

    I could come up with 4 Ab initio good tools:
    1 - gilmmer3,
    2 - prodigal
    3 - genemark.hmm
    4 - genemarkS

    Easygenes/Fgenes: I am not sure of these, how good are these.
    However, I need to drop either GenemarkS or GeneMark.hmm.

    I am unable to figure out the criteria.
    GeneMarkS - gives start, stop, gene_name and strand.
    But it is the best for statistical data. Provides option to remove overlap. No sequence in nucleotide or amino acids

    GeneMark.hmm - gives gff outout, cannot remove overlap,
    Gives amino acids & nucleotide sequence.

    Other tools for validation - TriTISA is not working,
    Homology based - genewise, there are bugs in the .c files of it.

    I am confused if I should go for BLAST or BLAT and why.
    Last edited by bio_informatics; 02-06-2014, 11:04 PM.
    Bioinformaticscally calm

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