CMCompare webserver: comparing RNA families via covariance models

Area of Science:

• Bioinformatics
• Computational Biology
• Molecular Biology

Background:

• Covariance models are standard for identifying novel non-coding RNAs based on sequence and structure.
• The Rfam database currently contains models for 2208 RNA families.
• Testing for specificity, sensitivity, and uniqueness is crucial before database inclusion.

Purpose of the Study:

• To introduce the CMCompare webserver (CMCws) for comparing Infernal RNA family models.
• To identify RNA models with poor specificity and explore relationships between models.
• To facilitate the avoidance of duplicate non-coding RNA family models.

Main Methods:

• The CMCompare webserver (CMCws) facilitates homology searches using covariance models.
• It compares user-generated models against the entire Rfam database.
• CMCws offers visualization tools to explore relationships between multiple RNA family models.

Main Results:

• CMCws identifies RNA models with poor specificity, ensuring accurate non-coding RNA identification.
• It aids in discovering relationships between RNA families, potentially revealing biological connections.
• The webserver helps prevent the creation of redundant models for existing non-coding RNA families.

Conclusions:

• The CMCompare webserver is a valuable tool for non-coding RNA research.
• It enhances the quality control and discovery process for RNA family models.
• CMCws supports the organization and understanding of RNA families and their potential clans.