SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Extract sequence from multi fasta file with PERL andreitudor Bioinformatics 27 07-07-2019 07:45 AM
Parsing multi fasta sequence file using Perl newbie2this Bioinformatics 9 09-11-2013 04:48 AM
Filter multi-fasta by length hchang10 Bioinformatics 4 06-18-2013 07:00 PM
Does Picard tool support multi-fasta file? ikarus97 Bioinformatics 2 05-13-2013 04:59 PM
Make Multi-fasta with annotations detq182 Bioinformatics 4 04-15-2012 05:50 AM

Reply
 
Thread Tools
Old 02-13-2014, 01:18 AM   #1
neha
Member
 
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
neha is offline   Reply With Quote
Old 02-13-2014, 01:50 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
Default

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.
GenoMax is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:25 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO