SNPs_analysis

[mmmm]

Dear all, I have 2 draft genomes of bacteria assembled by velvet and I used Mauve to extract snps (but I need your advice to:
- know if these snps are synonomas or nonsynonomas
-in which genes they are located?

is there a softwrae that can do this?

(I know snpeff- can be used but I do not have a reference strain)

your advice is very appreciated

[TiborNagy]

First you need to create an annotation (RAST) and after that you can use snpeff.

[mmmm]

thanks- have created the annotation using RAST on the draft genome- now how to us the annotation file in snpeff (can I download the genbank file to snpeff database)???

[BurlEarl]

This is a pain. To add a custom genome to SnpEff you need to add lines to the snpEff.config file. There is good documentation here:

http://snpeff.sourceforge.net/SnpEff_manual.html#databases

Under building databases. It is a little picky.

i added lines to snpEff.config like this:

#Friend Murine Leukemia Virus
X02794.genome : FMuLV

cd PATH/TO/snpEff/data
mkdir X02794
cp PATH/TO/GENBANKFILE/genes.gb X02794/genes.gb

java -jar snpEff.jar build -genbank -v X02794

I think that is what i did...Anyway, documentation is pretty good. I remember having a problem with my generated .gb file. Turns out there needed to be a couple of spaces after ORIGIN and the sequence.

good luck