tRNAmod

The tRNAmod is a freely available and user friendly web-server, where any user can predicts Uridine-modifications in their tRNA sequences (or whole genome). This page will help users to explore all available options in the tRNAmod so they can use it efficiently.

tRNAmod provides two different level of predicitons: (1) Sequence level prediction and (2) Genome-wide prediction.

1. Sequence level prediction
In the sequence level prediction, tRNAmod requires tRNA sequences in FASTA format and it will predict Uridine-modifications in the given tRNAs.

2. Genone-wide prediction
In the Genome-wide prediction, user can submit whole genome as an input. First tRNAmod will extract tRNA sequence from given genome using tRNAscan-SE software than it will predict Uridine-modifications in each tRNA separately.

Job Title [optional]: User can give a specific name for job title.

E-mail [optional]: After job completion, all the prediction results will also send to the given Email ID of user.

Input sequence: The tRNAmod accepts tRNA sequence (or whole genome) only in standard FASTA format (User can submit/upload multiple tRNA sequences).

Source of tRNAs (only for Genome-wide prediction): Please select appropriate source tRNA option from these eight available options.
1. Any (default)
2. Archaeal tRNAs
3. Bacterial tRNAs
4. Eukaryotic (All) tRNAs
5. Eukaryotic (cytosolic) tRNAs
6. Eukaryotic (mitochondrial) tRNAs
7. Eukaryotic (plastidic) tRNAs
8. Viral tRNAs

Prediction approach: Please select prediction approach of either hybrid (recommended) or binary. Hybrid approach is more accurate but it requires tRNA structure. Although, our web-sever predicts tRNA structure using tRNAscan-SE but sometime it fails to predict. Therefore, as an alternate binary approach can be use.

SVM Threshold Options: The performance of SVM is threshold-dependent and users can choose SVM thresholds according to their use. The default threshold is 0.0.

Probability Score: tRNAmod gives a probability score (range 0-9) for each predicted modified Uridines. Higher probability score means probability of correct prediction is high and vice-versa.

Prediction results of tRNAmod: tRNAmod will display modified Uridines in blue color. It gives single letter code Y, D, T and U for Pseudo-uridine, Dihydro-uridine and 5-methyl-Uridine and any modified-Uridine respectively. It also predicted tRNA structures with the help of tRNAscan-SE and draw tRNA structures by VARNA Visualization Applet.