NetStart 1.0c – Translation Start in Vertebrate & A. Thaliana DNA

NetStart 1.0c

:: DESCRIPTION

NetStart produces neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences. NetStart has been trained on cDNA-like sequences and will therefore presumably have better performance for cDNAs and ESTs. We have not tested the performance on genome data which may contain introns adjacent to the start codon.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetStart

:: MORE INFORMATION

Citation

Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis.
A. G. Pedersen and H. Nielsen, ISMB: 5, 226-233, 1997.

MetaTISA – Translation Initiation Site Annotation for Metagenomes

MetaTISA

:: DESCRIPTION

MetaTISA is tool with an aim to improve translationa initiation sites (TISs) prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict TISs by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 MetaTISA

:: MORE INFORMATION

Citation

Gang-Qing Hu, Jiang-Tao Guo, Yong-Chu Liu, and Huaiqiu Zhu.
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.
Bioinformatics 2009,25(14):1843-1845.

SATRAP 0.2 – SOLiD Assembler TRAnslation Program

SATRAP 0.2

:: DESCRIPTION

SATRAP is a computer program designed to efficiently translate de novo assembled color-space sequences into a base-space format.

::DEVELOPER

CRIBI Biotechnology Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SATRAP

:: MORE INFORMATION

Citation

SATRAP: SOLiD Assembler TRAnslation Program.
Campagna D, Gasparini F, Franchi N, Manni L, Telatin A, Vitulo N, Ballarin L, Valle G.
PLoS One. 2015 Sep 14;10(9):e0137436. doi: 10.1371/journal.pone.0137436.

Bagheera – Predicting Fungal CUG Codon Translation in Yeast

Bagheera

:: DESCRIPTION

Bagheera is a web server of prediction of genes in yeast species by providing the correct CUG decoding scheme , that allows determining the most probable CUG codon translation for a given transcriptome or genome assembly based on extensive reference data.

::DEVELOPER

Bagheera team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014 May 29;15:411. doi: 10.1186/1471-2164-15-411.
Predicting the fungal CUG codon translation with Bagheera.
Mühlhausen S, Kollmar M

BioPAX2SBML – Translation of BioPAX into SBML including the Qualitative Models extension

BioPAX2SBML

:: DESCRIPTION

BioPAX2SBML is a  webtool. It is capable of properly translating BioPAX formats (Level 2 and 3) into SBML format (Level 3 Version 1 with qual) including reactions and relations in one model.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

   NO

:: MORE INFORMATION

Citation

Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, and Zell A.
Qualitative translation of relations from BioPAX to SBML.
Bioinformatics (2012) 28 (20): 2648-2653.

Synergizer – Provide Translations of Biological Database Identifiers

Synergizer

:: DESCRIPTION

The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a “namespace”) to another.

::DEVELOPER

Roth Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Synergizer for Perl , for Java

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Oct 1;24(19):2272-3. Epub 2008 Aug 12.
The Synergizer service for translating gene, protein and other biological identifiers.
Berriz GF, Roth FP.