TitleFinding non-coding RNAs through genome-scale clustering.
Publication TypeJournal Article
Year of Publication2009
AuthorsTseng H-H, Weinberg Z, Gore J, Breaker RR, Ruzzo WL
JournalJournal of bioinformatics and computational biology
Date or Month Published2009 Apr
KeywordsChromosome Mapping, Cluster Analysis, Genome, RNA, Untranslated, Sequence Analysis, RNA
AbstractNon-coding RNAs (ncRNAs) are transcripts that do not code for proteins. Recent findings have shown that RNA-mediated regulatory mechanisms influence a substantial portion of typical microbial genomes. We present an efficient method for finding potential ncRNAs in bacteria by clustering genomic sequences based on homology inferred from both primary sequence and secondary structure. We evaluate our approach using a set of predominantly Firmicutes sequences. Our results showed that, though primary sequence based-homology search was inaccurate for diverged ncRNA sequences, through our clustering method, we were able to infer motifs that recovered nearly all members of most known ncRNA families. Hence, our method shows promise for discovering new families of ncRNA.
Downloadshttp://www.ncbi.nlm.nih.gov/pubmed/19340921?dopt=Abstract Abstract
Alternate JournalJ Bioinform Comput Biol
Citation Key1867
PubMed ID19340921