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Table 1 Scoring matrix used by irScan's IR detector

From: A framework for automated enrichment of functionally significant inverted repeats in whole genomes

  A C G U N
A 5 -4 -4 -4 0
C -4 5 -4 -4 0
G -2 -4 5 -4 0
U -4 -2 -4 5 0
N 0 0 0 0 3
  1. The local alignment scoring matrix used when aligning a nucleotide sequence against its reverse complement. Matches score 5 points, while mismatches are penalized by 4. All unresolved ambiguous loci are treated as an N regardless of which bases are more probable. This matrix appears to work best at predicting the secondary structures of the known 190 pre-miRNA. Note that G-A and U-C mismatches are not penalized as much to accommodate the occurrence of G-U and U-G base pairs respectively.