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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