Blast2GO allows searching for non-coding RNA (ncRNA) families and other structured RNA elements sequences via the RFAM webservice. The RFAM database is a collection of RNA families, categorized into three functional classes:
- non-coding RNA genes
- structured cis-regulatory elements
- self-splicing RNAs
The RFAM algorithm allows via alignments to search this database and classify your sequence dataset. This might be interesting for contigs obtained via de-novo RNAseq, especially sequences with no similarity to any known proteins (no blast results – red sequences).
The video shows how to run RFAM and interpret its results. Available summary charts are shown and explained.