MINTbase V2 – Exploration of Mitochondrial and Nuclear tRNA Fragments

MINTbase V2

:: DESCRIPTION

MINTbase: a web-based framework that serves the dual-purpose of being a content repository for tRFs and a tool for the interactive exploration of these newly discovered molecules.

::DEVELOPER

the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

MINTplates

:: MORE INFORMATION

Citation

Pliatsika, V, Loher, P, Telonis, AG, Rigoutsos, I.
MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments
Bioinformatics. 2016; In press.

ARWEN 1.2.3 – tRNA Detection in Metazoan Mitochondrial Sequences

ARWEN 1.2.3

:: DESCRIPTION

ARWEN is the software that identifies tRNA genes in metazoan mitochondrial nucleotide sequences. ARWEN detects close to 100% of previously annotated genes.

::DEVELOPER

ARWEN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ARWEN

:: MORE INFORMATION

Citation

Laslett, D. & Canbäck B. (2008)
ARWEN, a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.
Bioinformatics 24;172-175

ARAGORN 1.2.41 – tRNA (and tmRNA) Detection

ARAGORN 1.2.41

:: DESCRIPTION

ARAGORN is a program to detect tRNA genes and tmRNA genes in nucleotide sequences

::DEVELOPER

ARAGORN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ARAGORN

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jan 2;32(1):11-6. Print 2004.
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.
Laslett D1, Canback B.

tRNAmod – Prediciton of tRNA Modifications

tRNAmod

:: DESCRIPTION

The tRNAmod is a web-server for the prediction of transfer RNA (tRNA) modifications. Post-transcriptional modifications of tRNA plays a major role in their functionality. It provides both flexibility as well as rigidity and fine tune tRNA structure for the maximum performance.

::DEVELOPER

tRNAmod team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Prediction of uridine modifications in tRNA sequences.
Panwar B, Raghava GP.
BMC Bioinformatics. 2014 Oct 2;15:326. doi: 10.1186/1471-2105-15-326.

icaars – Identification & Classification of Aminoacyl tRNA Synthetases

icaars

:: DESCRIPTION

icaars – Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains.

::DEVELOPER

icaars team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Sep 22;11:507. doi: 10.1186/1471-2164-11-507.
Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains.
Panwar B1, Raghava GP.

MARSpred – Prediction of Mitochondrial Aminoacyl tRNA Synthetases

MARSpred

:: DESCRIPTION

MARSpred is a prediction method for discrimination between Mitochondrial-AARSs and Cytosolic-AARSs.

::DEVELOPER

MARSpred team.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Amino Acids. 2012 May;42(5):1703-13. doi: 10.1007/s00726-011-0872-8. Epub 2011 Mar 13.
Predicting sub-cellular localization of tRNA synthetases from their primary structures.
Panwar B1, Raghava GP.

tRNAmodpred – Predicting Posttranscriptional Modifications in tRNAs

tRNAmodpred

:: DESCRIPTION

tRNAmodpred is a method for predicting modifications in tRNA using the MODOMICS database of RNA modification pathways as a reference.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

tRNAmodpred

:: MORE INFORMATION

Citation:

tRNAmodpred: a computational method for predicting posttranscriptional modifications in tRNAs.
Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM.
Methods. 2016 Mar 22. pii: S1046-2023(16)30047-0. doi: 10.1016/j.ymeth.2016.03.013.

FindtRNA 1.0 – tRNA Prediction tool

FindtRNA 1.0

:: DESCRIPTION

The program FindtRNA idntifies tRNA genes without introns or with introns at canonical positions or also at non-canonical positions. The program employs algorithm to find number of tRNA(s) present in the supplied genome sequence and predict the tRNA secondary (cloverleaf) structure of those tRNAs.

::DEVELOPER

Dipanwita Paul, Md. Aftabuddin

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
Java

:: DOWNLOAD

FindtRNA

:: MORE INFORMATION

SPLITS 1.1 / SPLITSX – tRNA Detection in Genome Sequence

SPLITS 1.1 / SPLITSX

:: DESCRIPTION

SPLITS and SPLITSX, expansion programs for tRNAscan-SE to detect spliced-tRNA genes, such as split-tRNA genes (Figure A) and intron-containing tRNA genes (Figure B) in archaea.

The length of the query sequence should be limited within 5 mega base pairs (nucleotide). If your sequence is longer than this, please divide the sequence and submit separately. Finally these programs are under active development. If you use these programs, please help me out by e-mailing me with suggestions, comments, and bug reports.

::DEVELOPER

Institute for Advanced Biosciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Perl

:: DOWNLOAD

SPLITS / SPLITSX

:: MORE INFORMATION

Citation

Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, Kanai A. (2006).
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.
In Silico Biology. 6, 0039.

Sugahara J., Yachie N., Arakawa K., Tomita M. (2007)
In Silico Screening of Archaeal tRNA-encoding Genes Having Multiple Introns with Bulge-Helix-Bulge Splicing Motifs,
RNA; 13: 671-681