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Old 09-23-2013, 01:47 PM   #1
Daniel Fernandez
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Location: Lima. Perú

Join Date: Nov 2011
Posts: 31
Default Glimmer: Multifasta analysis

Hi everyone.
I am new user at glimmer. We have a bacterial genome in multifasta, contigs. We can predict the ORF, if we could a complete genome in one fasta, we could, but we with Multifasta, we can make a a lot of things and I'm pretty sure that we're wrong.

First, we separate the Genome.fas in 128 fasta files (beacuse it has 128 sequences), for make a *.train file we create a lot of *.train for any contig and put them all together in one file run.train

Code:
long-orfs -n -t 1.15 Contig1 run1.longorfs && extract -t Contig1 run1.longorfs > run.train
...
long-orfs -n -t 1.15 Contig128 run128.longorfs && extract -t Contig128 run128.longorfs >> run.train
then we create a *.icm model

Code:
build-icm -r model.icm < run.train
but I compared it with other analysis of my friend, for he, all *logorfs are the same name, so he replace in any line this file. But my friend and my, we can the SAME NUMBER OF ORF!!!.

Code:
long-orfs -n -t 1.15 Contig1 run1.longorfs && extract -t Contig1 run1.longorfs > run.train
...
long-orfs -n -t 1.15 Contig128 run1.longorfs && extract -t Contig128 run1.longorfs >> run.train
Code:
build-icm -r model.icm < run.train
So, my friend and my, we can the SAME NUMBER OF ORF!!! although we did diferent things. I'm pretty sure that we're wrong.

So. How do you analyse MultiFasta with Glimmer?
And how do yu extract the fasta from *.predict file in mulifasta?

Please, healp.
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