Hi Mathieu,

Mauve (http://asap.ahabs.wisc.edu/mauve/) is a nice tool for performing
multiple genome alignments on microbial genomes.  You should be able to
quickly see if any of the contigs are unique to your strain.  It's pretty
easy to extract the aligned regions from the Mauve output if you're familiar
with parsing fasta files.

Also, a group at the Army Research Lab recently released a tool for finding
PCR-based markers (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905370/).  I
haven't tried it yet so I'm not sure how useful it would be to you.

Errol Strain
FDA - Center for Food Safety and Applied Nutrition


On Tue, Aug 10, 2010 at 10:45 AM, Mathieu Parent
<parent.mathieu@gmail.com>wrote:

> Hi,
>
> I am currently working on a project where we used 454 sequencing to get the
> complete genome of a bacterial strain, a Lactobacillus reuterei. The
> results
> came back as about 100 contigs, for a total of 1.8Mb over the total 1.8Mb
> of
> the genome.
>
> My question is to know if I could use bioconductor to run an alignement of
> the two complete published genomes from NCBI and then get an alignment of
> my
> contigs on this.
>
> The goal is to develop a strain specific qPCR primer that will cover a
> sequence unique for our genome.
>
> Two approaches.
> 1. I could blast the whole genome in small chunks, rank it in score and
> select the top100 or top50
> 2. I could align them, visualise it with a genome browser and find
> deletions
> or unique sections.
>
> I have experience with bioconductor for microarray analysis and an
> intermediate knowledge of R.
>
> Thanks for any advice you all might have on the approach as well as the
> packages I could possibly use to execute them.
>
> Best Regards,
> Mathieu
> McGill University
>
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