running Glimmer3.02 on multi-fasta file

[neha]

Hello everyone,

I have around 2000 bacterial contigs obtained after de novo assembly. I want to annotate them using glimmer. Glimmer takes one contig at a time and predicts gene but I want that it should predict the genes in multi-fasta file together as there may be some genes overlapping in contigs which could be missed if I do gene prediction in one one contig separately.

Please suggest how to do this.

Hoping for a positive response

Thanks and Regards,
Neha

[GenoMax]

Not answering your question about glimmer but this question was discussed in a recent thread. Perhaps you can use one of the options there: http://seqanswers.com/forums/showthread.php?t=40639

BTW: Is this a single bacterial genome or more than one? 2000 contigs is a lot for a single bacterial genome.