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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.
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.
