miRNAminer

This is a DEVELOPMENT version!
The live version is at http://pag.csail.mit.edu/mirnaminer

miRNAminer is a web-based tool used for homologous miRNA gene search in several species. Given a search query, candidate homologs are identified using BLAST search and then tested for their known miRNA properties, such as secondary structure, energy, alignment and conservation, in order to assess their fidelity. Default parameters are stringent, though these can be relaxed. miRNAminer can be used prior to depositing novel miRNAs in public databases (such as miRbase).

Updates:
18 Feb 2008: miRNAminer has been updated to ENSEMBL version 48
18 Feb 2008: miRNAminer search now includes Platypus (ornithorhynchus anatinus)

max RNA fold energy (delta G)

minimal length of precursor sequence (nt)

maximal length of precursor sequence (nt)

minimal base pairing percentage in miRNA precursor

maximal number of gaps in miRNA precursor alignment

minimal identity percentage in miRNA precursor alignment

maximal overlap of mature miRNA and hairpin (nt)

minimal mature miRNA identity

minimal BLAST alignment length (nt)

maximal number of mismatches in mature miRNA

maximal BLAST e-value

number or results to report

Require seed conservation in mature miRNA (nt 2-8)

Target genomes (hold Ctrl and click to select more than one):

MicroRNA precursor sequence (required):

Mature microRNA sequence (required):

Optional: your email address (results will be sent to that email)

When you're ready, press Submit and wait for the result screen (search time depends on the number of requested results and the number of searched genomes)

Contact mirnaminer@gmail.com with questions or concerns about miRNAminer.

When referring to miRNAminer please quote the following reference
Shay Artzi, Adam Kiezun and Noam Shomron. miRNAminer: a tool for homologous microRNA gene search. BMC Bioinformatics 2008, 9:39
http://www.biomedcentral.com/1471-2105/9/39