Resources

Databases

mirbase

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.

[miRBase papers]

 

Rfam

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.

[Rfam papers]

 

RNAcentral

miRBase is part of the RNAcentral Consortium. RNAcentral is an integrated database of non-coding RNA sequences — a kind of Uniprot for RNAs.

[RNAcentral papers]

 

Software

ralee

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.

[RALEE paper]

 

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.

[SeqTrimMap paper]

 

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.

[EmpiricalGO paper]