bacterial genome annotation for rna seq analysis

Question

[slimane.khayi]

Dear all,

I have performed transcriptomic experiment for 3 bacterial strains. I have the the complete sequence genome of these strains that are homogeneous except some few SNPs between their genomes. One of these genome is annotated and I want to annotate the two others in order to conserve the same name of the genes for RNA-seq analysis. If you have a methodology suggestion I''ll be thankful.

[Naren]

For all the three Try MG-RAST for metagenomic annotations

Answer 1

[thackl]

MAKER's map2assembly might be able to do what you want. However, installing maker might be a bit over the top...

Usage:
     map2assembly <genome.fasta> <transcripts.fasta>
     Maps old gene models to a new assembly where possible.