An artificial functional family filter in homolog searching in next-generation sequencing metagenomics.

ABSTRACT: In functional metagenomics, BLAST homology search is a common method to classify metagenomic reads into protein/domain sequence families such as Clusters of Orthologous Groups of proteins (COGs) in order to quantify the abundance of each COG in the community. The resulting functional profile of the community is then used in downstream analysis to correlate the change in abundance to environmental perturbation, clinical variation, and so on. However, the short read length coupled with next-generation sequencing technologies poses a barrier in this approach, essentially because similarity significance cannot be discerned by searching with short reads. Consequently, artificial functional families are produced, in which those with a large number of reads assigned decreases the accuracy of func

SUBMITTER: Du R 

PROVIDER: S-EPMC3597637 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature