Databases
miRBase is the standard database of microRNA genes and annotation. The SGJlab is responsible for microRNA gene nomenclature, and for maintaining official lists of microRNAs in animal, plant and viral genomes.
Rfam is a database of non-coding RNA sequence alignments and derived covariance models. Its main use is identifying homologs of structured RNAs, including in assembled genomes. Rfam was founded by Sam Griffiths-Jones and Alex Bateman at the Wellcome Trust Sanger Institute with Sean Eddy at HHMI Janelia Farm. Rfam is managed by the Bateman lab at the EBI.
miRBase is part of the RNAcentral Consortium. RNAcentral is an integrated database of non-coding RNA sequences — a kind of Uniprot for RNAs.
YNCA
YNCA (the Yeast Non-Coding RNA Analysis site) is a catalogue of non-coding RNA gene knock-outs and relevant associated phenotypes in different growth media in Saccharomyces cerevisiae, produced in collaboration with the Delneri and O’Keefe labs in Manchester.
Software
RALEE — RNA ALignment Editor in Emacs — is a prototype RNA alignment editor implemented as a major mode for Emacs. It is particularly useful for viewing and editing relatively small multiple sequence alignments of structure RNA.
SeqTrimMap
SeqTrimMap is a bash script that maps reads from a small RNA deep sequencing dataset to a reference genome using the sequential trimming and mapping strategy described in Marco and Griffiths-Jones (2011). It is mostly useful for microRNA discovery and expression from AB SOLID datasets.
EmpiricalGO
EmpiricalGO is a Python script that generates the empirical distribution of the number of microRNA target genes in GO terms and returns p-values for term enrichment.