tRFtarget 2.0

Data Source

Human

• tRFs:
  • Human tRF-1s, tRF-3s and tRF-5s are retrieved from tRFdb (retrieving date November 15, 2019).
  • Human tsRNAs are download from a PNAS study.
• Transcripts: Human protein-coding transcript sequences (version GRCh38.p13) are download from GENCODE.
• Transcript Names: Human transcript names (version GRCh38.p13) corresponding to the Ensemble IDs are download from Ensembl BioMart.
• Approved Gene Symbols: Approved human gene symbols are download from HGNC BioMart (retrieving date November 14, 2019).

Mouse

• tRFs: Mouse tRF-1s, tRF-3s and tRF-5s are retrieved from tRFdb (retrieving date April 24, 2020).
• Transcripts: Mouse protein-coding transcript sequences (version GRCm38.p6) are download from GENCODE.
• Transcript Names: Mouse transcript names (version GRCm38.p6) corresponding to the Ensemble IDs are download from Ensembl BioMart.
• Gene Symbols: Mouse gene symbols are download from MGI (retrieving date April 24, 2020).

Drosophila Melanogaster

• tRFs: Drosophila Melanogaster tRF-1s, tRF-3s and tRF-5s are retrieved from tRFdb (retrieving date June 13, 2020).
• Transcripts: Drosophila Melanogaster protein-coding transcript sequences (version BDGP6.28) are download from Ensembl BioMart.
• Gene Symbols: Drosophila Melanogaster gene symbols (version BDGP6.28) are download from Ensembl BioMart.

Caenorhabditis elegans (C. elegans)

• tRFs: C. elegans tRF-3s and tRF-5s are retrieved from tRFdb (retrieving date June 19, 2020).
• Transcripts: C. elegans protein-coding transcript sequences (version WBcel235) are download from Ensembl BioMart.
• Gene Symbols: C. elegans gene symbols (version WBcel235) are download from Ensembl BioMart.

Schizosaccharomyces pombe (S. pombe)

• tRFs: S. pombe tRF-1s, tRF-3s and tRF-5s are retrieved from tRFdb (retrieving date June 27, 2020).
• Transcripts: S. pombe protein-coding transcript sequences (version ASM294v2) are download from EnsemblFungi BioMart.
• Gene Symbols: S. pombe gene symbols (version ASM294v2) are download from EnsemblFungi BioMart.

Rhodobacter sphaeroides ATCC 17025 (R. sphaeroides)

• tRFs: R. sphaeroides tRF-3s and tRF-5s are retrieved from tRFdb (retrieving date June 28, 2020).
• Transcripts: R. sphaeroides protein-coding transcript sequences (version ASM1640v1) are download from EnsemblBacteria.

Xenopus tropicalis (tropical clawed frog)

• tRFs: Xenopus tropicalis tRF-1s, tRF-3s and tRF-5s are retrieved from tRFdb (retrieving date July 4, 2020).
• Transcripts: Xenopus tropicalis protein-coding transcript sequences (version Xenopus_tropicalis_v9.1) are download from Ensembl BioMart.
• Transcript Names: Xenopus tropicalis transcript names (version Xenopus_tropicalis_v9.1) corresponding to the Ensemble IDs are download from Ensembl BioMart.
• Gene Symbols: Xenopus tropicalis gene symbols (version Xenopus_tropicalis_v9.1) are download from Ensembl BioMart.

Zebrafish (Danio rerio)

• tRFs: Zebrafish tRF-1s, tRF-3s and tRF-5s are retrieved from tRFdb (retrieving date July 6, 2020).
• Transcripts: Zebrafish protein-coding transcript sequences (version GRCz11) are download from Ensembl BioMart.
• Transcript Names: Zebrafish transcript names (version GRCz11) corresponding to the Ensemble IDs are download from Ensembl BioMart.
• Gene Symbols: Zebrafish gene symbols (version GRCz11) are download from Ensembl BioMart.

Prediction Tools Setting

The computational predicted binding interactions between human tRFs and target transcripts are based on the state-of-the-art prediction tools RNAhybrid and IntaRNA.

RNAhybrid

RNAhybrid is an old but still popular tool. It is a free energy-based tool, and utilizes the Dynamic Programming technique to efficiently calculate the optimal and more suboptimal interaction sites. The detailed setting of RNAhybrid are shown as below:

• Version: 2.1.2
• -b = 5, reported number of interaction sites on each transcript.
• -e = -15, free energy threshold.
• -m = 50000, maximum length of transcript. The default value is 50,000, so all transcripts with a longer length than 50,000 bases will be ignored and therefore have no RNAhybrid predictions in the tRFtarget database.
• Other parameters are set as default.
• Binding interactions with maximum complementary length less than 6 are filtered out (The definition of maximum complementary length can refer MANUAL).

IntaRNA

IntaRNA is also a free energy-based tool, and the only difference with RNAhybrid is IntaRNA incorporates the “accessibility” feature. The detailed setting of IntaRNA are shown as below:

• Version: 3.1.3
• --mode = M, running mode. Exact mode rather than Heuristic mode is used in order to get global minimum free energy interactions at the cost of consuming much more run time.
• --seedBP = 6, threshold of the number of base pairs within the seed sequences.
• -n = 5, number of (sub)optimal interactions to report.
• Other parameters are set as default.
• Similar Binding interactions are recognized as duplications and are filtered out (The definition of similarity between interactions can refer MANUAL).