Basic Info

Using the cmscan program in conjunction with Non-coding RNA family models from the Rfam database, search for and annotate potential Non-coding RNA sequences present in the genome

More Details

Non-coding RNA (ncRNA), which includes rRNA, tRNA, snRNA, snoRNA, and microRNA (miRNA) among others, is RNA that does not encode proteins. Instead, it directly exercises its biological functions at the RNA level after transcription, without requiring translation into proteins.

Rfam is a database of ncRNA families. It contains sequence and structural information for numerous ncRNA families, classified based on experimental evidence and computational predictions. The Rfam database not only provides a collection of ncRNA sequences but also includes annotations for these sequences, conserved secondary structural features, and information about their functions in organisms.

What's New

Cmscan is a program within the Infernal software package, which is designed for biological sequence analysis, particularly for RNA secondary structure alignment. Cmscan performs covariance models to search and align RNA sequences in sequence databases. These covariance models describe the characteristics of RNA sequences and their predicted secondary structures. During ncRNA annotation, Cmscan can identify sequences that match specific ncRNA families.

Additional Information

Related links:

http://eddylab.org/infernal/

https://rfam.xfam.org/

Literature

Kalvari I, Nawrocki EP, Ontiveros-Palacios N, et al. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 2021;49(D1):D192-D200. doi:10.1093/nar/gkaa1047

Eddy SR. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics. 2002;3:18. Published 2002 Jul 2. doi:10.1186/1471-2105-3-18