how to create annotation table

[paa6]

Currently, I am dealing with bacterial genome. I have tried to predict cds by glimmer, fgenesb and classic rast. Until now I was trying to create annotation table by comparing all cds by already mentioned software. In total I have 2,300 CDS. If I try by manual inspection it will take minimum 2 months. Is there any other possible way to generate annotation table in short time.

thanks in advance.

[GenoMax]

Prokka has been recommended as a good tool for annotation of bacterial genomes on the forum: http://www.vicbioinformatics.com/software.prokka.shtml

You can also use NCBI's prokaryotic genome annotation pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/) if you intend to make the sequence public.

[diego diaz]

What format are the annotation files ?

You have to choose some strategy to parse your files depending on the format.

For example, if your annotations are in gbk format, you can try some library like bioperl, biopython or biojava. If your files are in GTF, GFF, etc you can use awk, sed , etc.