LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.

ABSTRACT:

Background

The search for distant homologs has become an import issue in genome annotation. A particular difficulty is posed by divergent homologs that have lost recognizable sequence similarity. This same problem also arises in the recognition of novel members of large classes of RNAs such as snoRNAs or microRNAs that consist of families unrelated by common descent. Current homology search tools for structured RNAs are either based entirely on sequence similarity (such as blast or hmmer) or combine sequence and secondary structure. The most prominent example of the latter class of tools is Infernal. Alternatives are descriptor-based methods. In most practical applications published to-date, however, the information contained in covariance models or manually prescribed search patte

SUBMITTER: Will S 

PROVIDER: S-EPMC3716875 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature