Non synonymous SNP programs

[colindaven]

Hello everyone,

I'm looking for a decent program for SNP analysis. My starting point is (similar to) a pileup file with:

Genome position
Reference Base
New base call
etc

I need to find out if the SNPs produce synonymous or non-syn amino acid changes.

I could program something myself, but am sure this has been done a few times before.

Any suggestions ?

cheers

Colin

[mpiro]

Hello Colin,

Try SIFT nonsynonymous single nucleotide variants (genome-scale)
http://sift.jcvi.org/www/SIFT_chr_coords_submit.html

All you need is a small script to transform your pileup to one of its input formats, comma separated list of chromosome coordinates, orientation (1,-1) and alleles. see more:
http://sift.jcvi.org/www/chr_coords_example.html

mp

[colindaven]

Hi Mpiro,

thanks, that looks like a good tip.

The only issue - we re looking at a bacterium
Pseudomonas aeruginosa PA14 (NC_008463)

How do we get it to use this as a reference ? The syntax doesn t seem to be listed. The "Select organism" window doesn t allow alternatives.

Thanks

cheers
Colin

[Jose Blanca]

Hi:
We had a similar problem (snp processing) and we developed a library in python to deal with it.
If you're feeling brave and you want to use it you're more than welcome. We haven't added support for guessing if an snp is synonymous but maybe the pipeline system can be useful to you.
To take a look:

http://bioinf.comav.upv.es/svn/biolib/

Regards,

Jose Blanca

[colindaven]

Hi Jose,

without much docs as far as I can tell its probably easier to adapt some java code of my own. Especially seeing as I m not used to working with Python packages.

Thanks anyway though
Colin

[colindaven]

I wrote a simple pipeline for this myself.

It isn t the easiest to use but saves a lot of time ..

If you re interested just get in touch.

Colin

[elzed]

colindaven, have u worked it out?

Hi,

I have some chloroplast genome sequences for two ecotypes of the same plant species. And i have already located all the SNPs and Indels in contigs.
However, i have no idea how to decide which variation site lead to synonymous or non-synonymous changes.

Do you have any idea?

Thanks a lot.

[colindaven]

Dear all,

I have received some interest in people looking for non-synonymous SNPs. We do have a simple pipeline but have discovered a few small bugs so I don't want to distribute it at the moment. I think there must be scope for someone to have a proper crack at it, possibly using bioperl or biojava and simple GFF annotations.

This isn't what I've done, so it's probably not useful for most people.

I'll post later if I have time in the future to update the scripts and retest, but that won't be for some time.

Cheers
Colin

[Jose Blanca]

I am also interested in this topic. I would like to add this functionality to ngs_backbone. Any tip on this regard will be most welcomed.

[zbjorn]

I wrote a script that does this. It takes a Maq SNP file (can be adapted for any file with a nt coordinate, reference base and consensus base though), a GenBank XML file and a pileup file as input. It returns all the data in the Maq SNP input file, plus the amino acid change, the protein name, the corrected coverage depth at the base (because Maq only reports up to 255X coverage) and the allele frequency. It's written in Mathematica though, and I don't think many other bioinformatics folks use Mathematica. (I strongly support it however.) If anyone wants it, it's called SNiPnfo, at http://utopia.mit.edu/bi.html. Unlike any other similar script I've come across, it's not limited to a few organisms; this will work for any organism with an annotated GenBank entry.

-Zach