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Table 5 Mining the C. elegans genome for putative miRNA hairpins

From: In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

  Rejected miRNA hairpins a Clustered b (miRNAs/loci) Similar b (miRNAs/loci)
5 kb flanking sequence NA 132 15,514 - -
Similarity to mature miRNA c NA - - 132 937
No overlap with exons d 2 130 11,197 130 706
L = 1.0 87 45 80 - -
L >= 1e-5 15 - - 116 197
Exclude TRF overlap e 0 45 74 - -
Filter on 7 descriptors 6 - - 116 162
Exclude known miRNA loci 132 0 20 0 64
similarity positioned correctly f 18 - - 0 41
  1. a Rejected C. elegans miRNA hairpins by this step alone
  2. b Remaining cumulative number of C. elegans miRNA hairpins; remaining cumulative number of genomic hairpin loci
  3. c Similarity to a metazoan mature miRNA of at least 19 nt length with at most three mismatches
  4. d Cel-mir-354 is fully located in the final exon of Y105E8A.16; cel-mir-356 is largely located in the 3'utr of ZK652.2, but overlaps 6 nt with the final exon
  5. e At most 40 nt overlap with a repeat identified by Tandem Repeats Finder [47]
  6. f Similarity with mature miRNA may have at most 3 nt overlap with hairpin loop coordinates and at least 8 nt of the stem must separate the similarity from the end of the hairpin. Criteria are set according to the biological model of miRNA maturation from hairpins [3].