miRNAminer is a web-based tool used for homologous miRNA gene search.

Input fields include:

max RNA fold energy (delta G)
  Maximal energy for secondary RNA structure. Default -21 kcal/mol. Higher numbers indicate less stringent requirement.

minimal length of precursor sequence (nt)
  Minimal allowed length (number of nucleotides) of a miRNA precursor. Sequences shorter than this will not be considered. Default 70.

maximal length of precursor sequence (nt)
  Maximal allowed length (number of nucleotides) of a miRNA precursor. Sequences longer than this will not be considered. Default 180.

minimal base pairing percentage in miRNA precursor
  RNA sequences whose secondary fold base pairing percentage is lower than this number are not considered to be miRNA precursors. Default 55.

maximal number of gaps in miRNA precursor alignment
  When miRNAminer examines a miRNA precursor candidate, it aligns its sequence to the query sequence. This number is the maximal number of gaps in this alignment. Default 10.

minimal identity percentage in miRNA precursor alignment
  When miRNAminer examines a miRNA precursor candidate, it aligns its sequence to the query sequence. Candidates whose percentage of identity in this alignment is lower than this number are not considered to be miRNA precursors. Default 56.

maximal overlap of mature miRNA and hairpin (nt)
  miRNAminer computes secondary structure for candidate miRNA precursors. Valid precursors fold into a hairpin shape, i.e. stem-loop. The mature miRNA should be located on the stem, but it may overlap with the loop (i.e., hairpin). Candidate miRNAs whose mature miRNAs overlap with the hairpin on more than the indicated number of nucleotides are not considered to be miRNA precursors. Default 4.

minimal mature miRNA identity
  miRNAminer examines each miRNA precursor candidate by aligning the mature miRNA sequence for the query to the candidate. Candidate miRNA for whom that alignment has identity lower than the indicated number are not considered to be miRNA precursors. Default 0.8.

minimal BLAST alignment length (nt)
  miRNAminer identifies candidate miRNA precursors by BLASTing the query sequence over target genomes. BLAST hits must have at least the indicated number of nucleotides to be considered candidate miRNA precursors. Default 18.

maximal number of mismatches in mature miRNA
  miRNAminer examines each miRNA precursor candidate by aligning the mature miRNA sequence for the query to the candidate. Candidate miRNA for whom that alignment has more than this indicated number of mismatches in this alignment are not considered to be miRNA precursors. Default 3.

maximal BLAST e-value
  miRNAminer identifies candidate miRNA precursors by BLASTing the query sequence over target genomes. BLAST hits must have at most the indicated e-value to be considered candidate miRNA precursors. Default 0.05.

number of results to report
  miRNAminer will present this number of top miRNA identified candidates in the output file for each of the selected genomes. Default 1.

Require seed conservation in mature miRNA (nt 2-8)
  MiRNAminer examines each miRNA precursor candidate by aligning the mature miRNA sequence for the query to the candidate. This option indicates whether candidate miRNA precursors are required to have the seed sequence perfectly conserved. Default: Yes.

Target genomes
  Search will be performed on the selected genomes. Default Human.

microRNA precursor sequence
  Enter sequence in either DNA or RNA format.

mature microRNA sequence
  Enter sequence in either DNA or RNA format.

Relaxing search parameters:

 If you wish to perform searches with relaxed parameters (i.e. lower stringency) we suggest first trying the following searches independently, and then in combination.

  - increase 'number of results to report' from 1 (default) to 5
  - decrease 'minimal mature miRNA identity' from 0.8 (default) to 0.7
  - decrease 'minimal base pairing percentage in miRNA precursor' from 55 (default) to 40
  - change 'minimal/maximal length of precursor sequence (nt)' from 70-180 (default) to 50-250
  - increase 'maximal number of gaps in miRNA precursor alignment' from 10 (default) to 15
  - do not 'Require seed conservation in mature miRNA (nt 2-8)' (uncheck box)