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Old 02-13-2014, 01:18 AM   #1
Location: kolkata

Join Date: Oct 2011
Posts: 32
Default running Glimmer3.02 on multi-fasta file

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 is offline   Reply With Quote
Old 02-13-2014, 01:50 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,982

Not answering your question about glimmer but this question was discussed in a recent thread. Perhaps you can use one of the options there:

BTW: Is this a single bacterial genome or more than one? 2000 contigs is a lot for a single bacterial genome.
GenoMax is offline   Reply With Quote

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