Table 4 Descriptions of benchmark data files
File | Type | Source | Size | Description | Sequence identities |
|---|---|---|---|---|---|
rRNA.txt | rRNA | 5S ribosomal RNA database [34] | 10.8 KB | 45 metazoan rRNA sequences | High |
tRNA.txt | tRNA | GtRDB-Genomics tRNA Database | 2.06 KB | 14 tRNA from various eukaryotes | Medium |
miRNA.txt | microRNA | miRBase [35] | 328 KB | 1855 mammalian miRNAs obtained from the latest release of miRBase. | High |
evofold.txt | Mixed ncRNA | [36] | 3.72 MB | 47509 functional RNAs identified by Evofold, utilizing a comparative genomics method based on phylogenetic stochastic context-free grammars. | Low |
asRNA.txt | Mixed ncRNA | [37] | 148 KB | 97 putative antisense ncRNAs identified from cDNA and EST databases for human and mouse. | Low |
snoRNA.txt | snoRNA | snoRNA-LBME-db [38] | 82.5 KB | 411 human snoRNAs and scaRNAs selectedd from snoRNA-LBME-db (release 3, August 2006) | Low |
151Rfam.txt | Mixed ncRNA | Rfam database [10] | 40.7 KB | 151 non-coding RNA structures downloaded from Rfam, as collected by Do et al. for CONTRAfold training [39] | Low |