Program to relate SNPs to model genome annotation?

[pmiguel]

EMS-mutagenesis causes G->A and C->T transitions. In most cases large numbers of these lesions are produced per genome with only one being the source of mutant phenotype screened for.

I have a lists of 50-100 of these mutations/genome for a number of yeast strains as determined from a SOLiD sequencing run.

What is the recommended method to convert this information (single base change at a known genomic location) to gene name and effect on the gene (eg, synonymous--no change to protein sequence, 1 residue change to sequence, or truncation)? Seems like something that would already have been written.

--
Phillip

[Torst]

What is the recommended method to convert this information (single base change at a known genomic location) to gene name and effect on the gene (eg, synonymous--no change to protein sequence, 1 residue change to sequence, or truncation)? Seems like something that would already have been written.

The "consequences" module in our software Nesoni (*) does this... BUT it requires you to use the previous "shrimp" (align) and "consensus" (call) modules beforehand - all the modules share a folder of results. It is mainly useful for bacterial genomes, so perhaps not as useful to you.

If it is only subsitutions and not indels, it's a pretty simple BioPerl script to take your list and a Genbank file of the genome and test the effects on each CDS.

(*) Nesoni http://www.vicbioinformatics.com/software.nesoni.shtml

[pmiguel]

The "consequences" module in our software Nesoni (*) does this... BUT it requires you to use the previous "shrimp" (align) and "consensus" (call) modules beforehand - all the modules share a folder of results. It is mainly useful for bacterial genomes, so perhaps not as useful to you.

If it is only subsitutions and not indels, it's a pretty simple BioPerl script to take your list and a Genbank file of the genome and test the effects on each CDS.

(*) Nesoni http://www.vicbioinformatics.com/software.nesoni.shtml

Does it handle multiple exon genes okay? I notice you are primarily a bacterial informatics shop...

Thanks for the response,
Phillip

[Torst]

Does it handle multiple exon genes okay? I notice you are primarily a bacterial informatics shop...

Yes as I said we are bacteria focussed. Even in bacteria we have introns sometimes, and pseudo genes are often written as join(a..b,c..d) for the N-term and C-term "exons". Nesoni uses BioPython for the annotation retrieval, so it *may* work. I will talk to the primary author and find out; it probably isn't difficult to alter to work with join() features. You could try it on a small chromosome? (Assuming you have a server with enough RAM)

--Torst

[pmiguel]

Yes as I said we are bacteria focussed. Even in bacteria we have introns sometimes, and pseudo genes are often written as join(a..b,c..d) for the N-term and C-term "exons". Nesoni uses BioPython for the annotation retrieval, so it *may* work. I will talk to the primary author and find out; it probably isn't difficult to alter to work with join() features. You could try it on a small chromosome? (Assuming you have a server with enough RAM)

--Torst

Hi Torst,
Thanks again for you response. I ended up writing a script employing bioperl to do this. Initially I thought it would take me less time than acquiring and installing Nesoni. But since it took me several days to write and debug my code I was probably wrong.
Phillip