Table 3 Putative miRNAs identified using similarity search, structural search and ab initio prediction
Cell line count(normalized) | Blast search against miRNAs in local DB1 | HHMMR | RNAfold | Rfam/INFERNAL2 | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Candidate number | Genomic location | Kerat | SCC5 | score | Original read overlaps Helix? | Keal/mol | Family | ID | Strand | Bit score | Start | End | Original reads overlaps Helix? | |
1 | Intergenic | 3.9 | 9.6 | - | 0.67 | No | -72,10 | - | - | - | - | - | - | - |
2 | Intergenic | 46 | 82.5 | - | 0.69 | No | -64,49 | - | - | - | - | - | - | - |
3 | Intron | 4.4 | - | 0.69 | Partially | -51,30 | - | - | - | - | - | - | - | |
4 | Intergenic | 3.9 | 51.6 | - | 0.66 | Partially | -44,30 | MIR245 | RF00816 | + | 29.76 | 97 | 182 | Total |
5 | Intron | - | 8 | - | 0.7 | No | 53,52 | - | - | - | - | - | - | - |
6 | Intergenic | - | 4.8 | - | 0.66 | No | -48,90 | - | - | - | - | - | - | - |
7 | Intergenic | - | 78.9 | Original DB: smiRNAdb; Type: unclassified RNA QueryCov: 13%; SbjCov: 97% Id: 100% | 0.66 | No | -57,34 | - | - | - | - | - | - | - |
8 | Intron | - | 5.6 | Origianl DB: smiRNAdb; Type: miRNA; QueryCov: 11%; SbjCov: 96% Id: 100% | - | - | 57,10 | - | - | - | - | - | - | - |
9 | Intergenic | - | 11.2 | Original DB: smiRNAdb; Type: unclassified RNA; QueryCov: 13%; SubjectCov: 94%; Id: 100%; | 0.67 | Total | -35,35 | mir-450 | RF00708 | + | 30.4 | 32 | 112 | Parcial |
mir-245 | RF00816 | + | 29.76 | 35 | 120 | Parcial | ||||||||
10 | Intergenic | - | 4.8 | - | - | - | -122,82 | mir-689 | RF00871 | + | 66.15 | 17 | 91 | No |
11 | Intron | - | 4.8 | - | 0.66 | Total | -83,69 | - | - | - | - | - | - | - |
12 | Intron | - | 4.0 | Original DB: smiRNAdb; Type: unclassified RNA; QueryCov: 12%; SubjectCov: 100%: Id: 100% | 0.68 | Total | -50,30 | - | - | - | - | - | - | - |
13 | Intron | - | 15.2 | - | 0.67 | No | -94,14 | - | - | - | - | - | - | - |