Paper Info
Title
CMCompare webserver: comparing RNA families via covariance models.
Abstract
A standard method for the identification of novel non-coding RNAs is homology search by covariance models. Covariance models are constructed for specific RNA families with common sequence and structure (e. g. transfer RNAs). Currently, there are models for 2208 families available from Rfam. Before being included into a database, a proposed family should be tested for specificity (finding only true homolog sequences), sensitivity (finding remote homologs) and uniqueness. The CMCompare webserver (CMCws) compares Infernal RNA family models to (i) identify models with poor specificity and (ii) explore the relationship between models. The CMCws provides options to compare new models against all existing models in the current Rfam database to avoid the construction of duplicate models for the same non-coding RNA family. In addition, the user can explore the relationship between two or more models, including whole sets of user-created family models. Visualization of family relationships provides help in evaluating candidates for clusters of biologically related families, called clans. The CMCws is freely available, without any login requirements, at http://rna.tbi.univie.ac.at/cmcws, and the underlying software is available under the GPL-3 license.
Year
DOI
Venue
2013
10.1093/nar/gkt329
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
internet
RNA,Rfam,Biology,Visualization,Login,Genetics,Web server,Covariance
Journal
Volume
Issue
ISSN
41
W1
0305-1048
Citations 
PageRank 
References 
2
0.38
10
Authors
3
Name
Order
Citations
PageRank
Florian Eggenhofer1233.72
Ivo L. Hofacker21669131.57
Christian Höner Zu Siederdissen317113.01