INDEL searches!

Bionewb · 02-24-2009, 12:05 PM

Hello,

I'm a student at the University of Florida and am doing a research project with a PI at the university of Florida and I am trying to find INDELs in two evolved strains compared to an ancestor strain. I have the sequence data (done using 454) for both evolved strains and the ancestor strain. I've done numerous searches on google for free indel software but can't seem to get the few I've found to work. I was hoping that someone more experienced here might be able to point me in the right direction.

Specifically, I am comparing both evolved strains to the ancestor strain to find insertions and deletions both evolved laboratory strains have that the ancestor does not. (I assume we will then compare the evolved strains to one another, but that hasn't yet been revealed to me).

I apologize ahead of time if I didn't supply you with any information you might need to answer this question. Feel free to ask!

Thanks so much for any help.

William

swbarnes2 · 02-24-2009, 12:52 PM

I've used SOAP to find 1 and 2 base insertions. You could also try Velvet, which will assemble contigs without reference. You won't get full coverage of your sample Velvet contigs, but you'll get lots.

Otherwise, just look for little bits where the coverage gets notably crummy compared to its immediate neighbors. Maybe aligning with 0 errors allowed will help you see those spots.

kmcarr · 02-26-2009, 11:30 AM

William,

Why not use the reference mapping software which comes with the 454, gsMapper?

Bionewb · 02-26-2009, 11:47 AM

I would love to but do not have it! What I have to work with is a contig table prepared via CLC Genomics Workbench of both the ancestor wild type and the evolved laboratory strain. Annotation has been done for the genes and my current option is to scroll through all 4mil bps. These contig files can be exported as numerous file types (FASTA files and a few others..) and can be uploaded to other softwares, though...

The actual sequencing was done in a previous semester and sent off to be done via 454 elsewhere. We just learned about the principles behind the process and prepared the genomic library. I've done some extensive googling but it seems that most programs require knowledge of Mac command prompt or Linux/Unix.

Is their software available for free on their website? I'd definitely give it a try.

Thanks very much for all your help!

William

kmcarr · 02-26-2009, 12:34 PM

William,

It just dawned on me that you are at UF Gainsville. Have you checked with the folks at your ICBR facility there? They have bioinformaticians on staff which may be able to provide some guidance.

Bionewb · 02-26-2009, 12:43 PM

Absolutely! I am e-mailing them while begging you for solutions. ;0 Don't wanna keep all my eggs in one basket.

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02-24-2009, 12:05 PM	#1
Bionewb Junior Member Location: Gainesville, FL Join Date: Feb 2009 Posts: 3	INDEL searches! Hello, I'm a student at the University of Florida and am doing a research project with a PI at the university of Florida and I am trying to find INDELs in two evolved strains compared to an ancestor strain. I have the sequence data (done using 454) for both evolved strains and the ancestor strain. I've done numerous searches on google for free indel software but can't seem to get the few I've found to work. I was hoping that someone more experienced here might be able to point me in the right direction. Specifically, I am comparing both evolved strains to the ancestor strain to find insertions and deletions both evolved laboratory strains have that the ancestor does not. (I assume we will then compare the evolved strains to one another, but that hasn't yet been revealed to me). I apologize ahead of time if I didn't supply you with any information you might need to answer this question. Feel free to ask! Thanks so much for any help. William

02-24-2009, 12:52 PM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	I've used SOAP to find 1 and 2 base insertions. You could also try Velvet, which will assemble contigs without reference. You won't get full coverage of your sample Velvet contigs, but you'll get lots. Otherwise, just look for little bits where the coverage gets notably crummy compared to its immediate neighbors. Maybe aligning with 0 errors allowed will help you see those spots.

02-26-2009, 11:30 AM	#3
kmcarr Senior Member Location: USA, Midwest Join Date: May 2008 Posts: 1,178	William, Why not use the reference mapping software which comes with the 454, gsMapper?

02-26-2009, 11:47 AM	#4
Bionewb Junior Member Location: Gainesville, FL Join Date: Feb 2009 Posts: 3	I would love to but do not have it! What I have to work with is a contig table prepared via CLC Genomics Workbench of both the ancestor wild type and the evolved laboratory strain. Annotation has been done for the genes and my current option is to scroll through all 4mil bps. These contig files can be exported as numerous file types (FASTA files and a few others..) and can be uploaded to other softwares, though... The actual sequencing was done in a previous semester and sent off to be done via 454 elsewhere. We just learned about the principles behind the process and prepared the genomic library. I've done some extensive googling but it seems that most programs require knowledge of Mac command prompt or Linux/Unix. Is their software available for free on their website? I'd definitely give it a try. Thanks very much for all your help! William

02-26-2009, 12:34 PM	#5
kmcarr Senior Member Location: USA, Midwest Join Date: May 2008 Posts: 1,178	William, It just dawned on me that you are at UF Gainsville. Have you checked with the folks at your ICBR facility there? They have bioinformaticians on staff which may be able to provide some guidance.

02-26-2009, 12:43 PM	#6
Bionewb Junior Member Location: Gainesville, FL Join Date: Feb 2009 Posts: 3	Absolutely! I am e-mailing them while begging you for solutions. ;0 Don't wanna keep all my eggs in one basket.