Table 1 TsRNAs-related databases or tools

tRFdb

The first tRFs database, providing genomic coordinates and names of tRNAs from which tRFs sequences are likely derived.

http://genome.bioch.virginia.edu/trfdb/

[92]

MINTbase v2.0

It can quickly filter tRFs by minimum abundance thresholds and tissue keywords, and provides the maximum abundance of tRFs as well as the related data information.

http://cm.jefferson.edu/MINTbase/

[93]

MINTmap

It contains data sets of tRFs encoded by mitochondria and nuclei, allows rapid identification of tRFs sequences, and calculates the raw and normalized abundance of tRFs.

https://github.com/TJU-CMC-Org/MINTmap/

[94]

tDRmapper

It provides a nomenclature system to define and quantify tDRs, which helps to discover new tDRs and explore more relevant biological functions.

https://github.com/sararselitsky/tDRmapper

[95]

tRFexplorer

It can visualize tRFs expression profiles in NCI-60 cell lines and TCGA tumor types, correlating with other ncRNAs expression profiles (e.g., miRNA) for patient survival correlation analysis.

https://trfexplorer.cloud/

[96]

PtRFdb

It provides 5607 unique tRFs sequences from 10 different plant species.

http://www.nipgr.res.in/PtRFdb/

[97]

tRF2Cancer

It quickly identifies tRFs by analyzing deep sequencing data and contains the expression of tRFs in different types of cancer.

http://rna.sysu.edu.cn/tRFfinder/

[98]

OncotRF

It provides a comprehensive view of tRFs dysregulated in cancers as well as their correlation with clinicopathological features.

http://bioinformatics.zju.edu.cn/OncotRF

[99]

tsRBase

It contains 121,942 tsRNAs from 20 organisms and combines the functional information of tsRNAs with their corresponding targets.

http://www.tsrbase.org

[100]

SPORTS1.0

It can analyze tsRNAs of multiple tissues/cell types, and predicts potential RNA modification sites based on nucleotide mismatches within tsRNAs.

https://github.com/junchaoshi/sports1.0

[101]