Format

Send to

Choose Destination
See comment in PubMed Commons below
RNA Biol. 2013 Jul;10(7):1170-9. doi: 10.4161/rna.25038. Epub 2013 May 20.

Computational identification of functional RNA homologs in metagenomic data.

Author information

1
Janelia Farm Research Campus; Ashburn, VA USA.

Abstract

A key step toward understanding a metagenomics data set is the identification of functional sequence elements within it, such as protein coding genes and structural RNAs. Relative to protein coding genes, structural RNAs are more difficult to identify because of their reduced alphabet size, lack of open reading frames, and short length. Infernal is a software package that implements "covariance models" (CMs) for RNA homology search, which harness both sequence and structural conservation when searching for RNA homologs. Thanks to the added statistical signal inherent in the secondary structure conservation of many RNA families, Infernal is more powerful than sequence-only based methods such as BLAST and profile HMMs. Together with the Rfam database of CMs, Infernal is a useful tool for identifying RNAs in metagenomics data sets.

KEYWORDS:

homology search; metagenomics; noncoding RNA; structural RNA

PMID:
23722291
PMCID:
PMC3849165
DOI:
10.4161/rna.25038
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Taylor & Francis Icon for PubMed Central
    Loading ...
    Support Center