Input RNA Sequences

tRFfinder supports only inputs in FASTA format. FASTA is a plain-text format for representing DNA, RNA or protein sequences. Every nucleotide or amino acid is represented by single-letter. For details on FASTA format, please see FASTA Format in Wikipedia.

For tRFfinder, only FASTA fromat for RNA sequences is supported. There are mainly two ways to input your sequence:

  1. Paste the sequence(s) into the input box. Be cautious that the sequences must be in FASTA format.


  2. Upload the file from your local hard drive. The "Choose File" button is for you!

After the input of RNA sequences reads in FASTA format, you can trun to "Advanced Options" for customization of parameters. For an example of input sequenes embedded in the software, please click the button.

Advanced Option for Parameters

In "Advanced Option", you can tune the parameter of tRFfinder.


  • Number of Allowed mismatch: The maximum number of mismatches allowed for mapping the small-RNA reads onto the tRNA. 0 by default, ranging from 0 - 2.

  • Allow Indel: "Indel" means insertion or deletion of nucleotide(s). This parameter sets the maximum number of nucleotide insertions or deletions allowed for mapping the small-RNA reads onto the tRNA sequences. "No" by default.

  • Shortest tRF Length (nt): Generally tRFs are of 16 nt in size. This parameter sets the minimum number of nucleotides (in contiguous positions on the tRNA) with p-values less than 0.01 required to be regarded as tRF candidates. 16 by default, ranging from 16 - 20.

  • Largest tRF Length (nt): Maximum length of the tRFs allowed to be regarded as tRF candidates. 28 by default, ranging from 28 - 35.

  • Selected P-value: 0.01 by default.

After clicking the button at the bottom of the page, you can view the result online. You can also enter your email address in the box above the button, than click . The result will be sent to you via email, as well as presented on web page.

Predict Results

It might take some time for tRFfinder to predict the tRFs. Please wait for a minute. On the "Predict Results" page, there are several important components.


  • Filter the result. Odds are that you want only to view the result of a specific tRF Type, like, tRF-novel. So you can enter "tRF-novel" and click "Enter", then come the results.

    You can also search or filter the results based on other keywords, like the Reads Number (RPM), tRF Length, Source tRNA, etc.

  • View Details. For details on the tRFs, you can click on the blue button. Then come the details of the tRFs. They are divided into three parts.

    1. Detailed Information of tRFs. This part includs information on Source tRNA Name, tRF Type, tRF Region, tRF Length, Reads Number (RPM) and the tRF Sequence.


      For more information on the source tRNA of the tRFs, you can click "Link to UCSC" or "Link to GtRNAdb".

    2. Reads Sequence Distribution on tRNAs. This shows how the tRF candidates are distributed along the tRNA sequence.


      There are three columns in this field. Every row show one specific small RNA reads, with the corresponding Read Length and Read Number. Atop this field is a tRNA sequence with part of it in red. This indicates the predicted position on the tRNA sequence that derives the tRFs. This prediction is based on the data below.

    3. Reads Number distribution on tRNAs Structure. This part shows the secondary structures of the tRNA, with the potential tRF sequence in red. (This function is based on the forna package ( ref. 1 )).


  • View Expression in Cancer Samples. For information on expression in different cancer samples, click the green button in the "Express in Cancers" column. For the manual on this function, see the "tRFinCancer" Section below.

  • tRF Browser. To see the distribution of tRFs in the genome, click the orange button. For the manual on this function, see the "tRFBrowser" Section below.

tRFinCancer

In tRFinCancer, you can see the expression profiles in 32 types of cancer samples.


The horizontal coordinate shows 32 types of cancer samples. The vertical coordinates shows the number of reads in the corresponding types of cancer samples. To download the profile result, click the button on the top-right corner. (See below.)


tRFBrowser

In tRFBrowser, you can view the distribution of the tRF across the human genome.


On the left of the panel, you can choose from 32 different types of cancer samples (called "tracks" in JBrowse). Then on the right of the panel, zoom in and zoom out to view the sequence details of tRFs.

Note that: Embedded in tRF2Cancer are 32 types of cancer, each type with varieties of samples. Because there are too many samples to show at one time, tRFBrowser randomly selects 10 samples to show at one time. It is reported that chemical modification in tRNA [5-methylcytosines (m5c), 2’-O-methylations (2’-O-Me), pseudouridine (Ψ), N6-Methyladenosine (m6A) etc.] might have an impact on generation of tRF. In addition to view the distribution of reads, you can also view the chemical modification on the tRNA.

References

[1] Kerpedjiev P, Hammer S, Hofacker IL. Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics. 2015 Oct 15;31(20):3277-9. doi: 10.1093/bioinformatics/btv372. Epub 2015 Jun 22. PubMed PMID: 26099263; PubMed Central PMCID: PMC4595900.