Tag: tRNA

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

 NO

:: 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

 NO

:: 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

 NO

:: 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