Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

ABSTRACT: Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. The emergence of new technologies for characterizing transcriptome outputs, notably RNA-seq, are improving noncoding RNA identification and expression quantification. However, a major challenge is to robustly distinguish functional outputs from transcriptional noise. To establish whether annotation of existing transcriptome data has effectively captured all functional outputs, we analysed over 400 publicly available RNA-seq datasets spanning 37 different A

SUBMITTER: Lindgreen S 

PROVIDER: S-EPMC4214555 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature