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. 2013 Oct 26;14:735. doi: 10.1186/1471-2164-14-735

Table 3.

Putative miRNAs identified using similarity search, structural search and ab initio prediction

 
  
 Cell line count(normalized)
 Blast search against miRNAs in local DB 1
HHMMR
 RNAfold
 Rfam/INFERNAL 2
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 - - - - - - -

Notation: Original DB: Database from which sequence was downloaded into local database: Type: RNA type (misRNA if not specified); Query Cov: percentage of database sequence covered in the alignment; Subject Cov: percentage of candidate covered by the alignment; Id: alignment identity; 1: local miRNA database with sequences from databases designated by the Non-coding RNA Databases Resource (NRDR).