Mapping against multiple sequences

[michaelDP]

Dear all,
I recently started working on soil metagenomics data and I am pretty ignorant in this area. I am trying to assign some NGS reads (Solid, Illumina, 454) to some reference bacterial genes I am interested in. For each of the reference gene, I have got hundreds of sequences that I have already aligned and now I would like to check if some of my reads corresponds these alignments.

As far as I know the taxonomic diversity of my samples are very high so I don't expect a very good coverage. So my first question is, is there a point to assemble my reads first ?

And my second question is, which tool would you recommend to assemble reads against multiple sequences ?

Regards,
Michael

[cliffbeall]

Metagenome analysis

As far as the assembly goes, I think its probably going to be difficult. It has been done in that recent MetaHIT nature paper, but they did have a lot of data, and I'm sure significant computing resources.

In terms of matching your aligned sequences, I think you can use a program like HMMer to make profile HMMs and look for matches in your translated reads. That should be more sensitive than BLAST.

[michaelDP]

Many thanks Cliffbeall,
at the moment I am using both BLAST and HMMer. I have tested the methods on simulated data and I am quite happy with the results.

Cheers,
Michael