Gene PredictionΒΆ
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. See the Prodigal home page for more info.
To run prodigal
on our data, simply type:
cd ~/workdir/assembly/megahit_out
qsub -cwd -N prodigal -l mtc=1 -b y \
/vol/biotools/bin/prodigal -p meta -a final.contigs.genes.faa -d final.contigs.genes.fna -f gff -o final.contigs.genes.gff -i final.contigs.fa
Output files:
final.contigs.genes.gff | positions of predicted genes in GFF format |
final.contigs.genes.faa | protein translations of predicted genes |
final.contigs.genes.fna | nucleotide sequences of predicted genes |