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Old 12-19-2014, 04:12 AM   #3
Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47

Hi Brian,
Yes basically, I am involved with a metagenomics study where I have 200-250bp sequence reads from Next Gen Sequencing derived from different regions of the 16s gene, i.e. 6 different primers (primer sequences are unknown as they are from a commercial kit and the company informed us that they are proprietary). For example, one fastq file that I have contains ~170K reads all from different regions of the 16s gene. I would like to be able to blast my reads against a database of bacteria so that in return I get each read aligned to the 16s gene somewhere and it's genomic coordinate, there I will know where a read in my file is derived form within the gene.

Does this make sense? The HOMD database ( allows one to blast a total of only 3000 reads. I am looking for a different tool that will allow me to blast all of my reads and will return the alignments, and percent identity along with where the read aligned along the gene.

JenBarb is offline   Reply With Quote