Tag: Gene Prediction

ChemGenome 2.1 – Gene Prediction Software

ChemGenome 2.1

:: DESCRIPTION

Chemgenome is an ab-intio gene prediction software, which find genes in prokaryotic genomes in all six reading frames. The methodology follows a physico-chemical approach and has been validated on 372 prokaryotic genomes.

::DEVELOPER

Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ChemGenome

:: MORE INFORMATION

Citation:

PLoS One. 2010 Aug 26;5(8):e12433.
A phenomenological model for predicting melting temperatures of DNA sequences.
Khandelwal G, Bhyravabhotla J.

YACOP 2 – Gene Prediction for Prokaryotes

YACOP 2

:: DESCRIPTION

YACOP is a metatool for gene prediction in prokaryotic genomes. The predictions generated by the tool are based on the output of existing gene finding programs. In present YACOP supports the boolean combination of predictions from Critica 105b (with wublast2), Glimmer 2.02 or Glimmer 2.10 (with RBSfinder), Orpheus (with dps) and ZCurve1.0. The output can be adapted to different modes by customizing the enclosed ini-file, so that the tool can also be used for comparision and evaluation of different predictions.

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

YACOP

:: MORE INFORMATION

Citation

M. Tech and R. Merkl (2003)
YACOP: Enhanced Gene Prediction Obtained by a Combination of Existing Methods
In Silico Biology 3:4.

IPred 201409 – Integrate ab initio and evidence based Gene Predictions

IPred 201409

:: DESCRIPTION

IPred (Integrate gene Predictions) is a program that combines the output of ab initio and evidence based (including comparative based) gene finders to improve on the overall prediction accuracy.

::DEVELOPER

IPred team

: SCREENSHOTS

IPred

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python
  • Java

:: DOWNLOAD

 IPred

:: MORE INFORMATION

Citation

BMC Genomics. 2015 Feb 26;16:134. doi: 10.1186/s12864-015-1315-9.
IPred – integrating ab initio and evidence based gene predictions to improve prediction accuracy.
Zickmann F, Renard BY

AUGUSTUS 3.4.0 – Gene Prediction for Eukaryotes

AUGUSTUS 3.4.0

:: DESCRIPTION

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server or be downloaded and run locally. It is open source so you can compile it for your computing platform.. This enables you to submit larger sequence files and allows to use protein homology information in the prediction. The MediGRID requires an instant easy registration by email for first-time users.

AUGUSTUS Online Version

::DEVELOPER

Mario Stanke and Oliver Keller , Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AUGUSTUS

:: MORE INFORMATION

Citation

Mario Stanke, Ana Tzvetkova, Burkhard Morgenstern (2006)
“AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome”
BMC Genome Biology, 7(Suppl 1):S11.

GenomeThreader 1.7.3 – Gene Prediction Software

GenomeThreader 1.7.3

:: DESCRIPTION

GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments.

:: DEVELOPER

GenomeThreader Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 GenomeThreader

:: MORE INFORMATION

Citation:

G. Gremme, V. Brendel, M.E. Sparks, and S. Kurtz.
Engineering a software tool for gene structure prediction in higher organisms.
Information and Software Technology, 47(15):965-978, 2005

FTG – Fast Fourier Transform based GENE Prediction Server

FTG

:: DESCRIPTION

FTG is aweb server for locating probable protein coding region in nucleotide sequence using fourier tranform approach

::DEVELOPER

FTG Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Issac, B., Singh, H., Kaur, H. and Raghava, G.P.S. (2002)
Locating probable genes using fourier transform approach.
Bioinformatics 18:196

MetaGUN 1.0 – Gene Prediction in Metagenomic Fragments based on the SVM Algorithm

MetaGUN 1.0

:: DESCRIPTION

MetaGUN is a novel gene prediction method for metagenomic fragments based on a machine learning approach of SVM.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

MetaGUN

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 5:S12. doi: 10.1186/1471-2105-14-S5-S12. Epub 2013 Apr 10.
Gene prediction in metagenomic fragments based on the SVM algorithm.
Liu Y, Guo J, Hu G, Zhu H.

MED 2.1 – Gene Prediction in Prokaryotic Genomes with Multivariate Entropy Distance method

MED 2.1

:: DESCRIPTION

MED is a non-supervised prokaryotic gene prediction method which integrates MED2.0 and TriTISA, an iterative self-learning translation initiation site (TIS) prediction algorithm. As the update of MED2.0, MED 2.1 modifies the TIS model by replacing the previous one to TriTISA, which imoroves the prediction accuracies for both 3′ and 5′ ends.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 MED

:: MORE INFORMATION

Citation

Zhu,H.Q. et al. 2007
MED: a new non-supervised gene prediction algorithm forbacterial and archaeal genomes.
BMC Bioinformatics,8, 97

Gangqing,Hu. Et al. 2009.
Prediction of translation initiation site for microbial genomes with TriTISA.
Bioinformatics 25,123-125.

Bcheck 0.6 – rnpB gene prediction

Bcheck 0.6

:: DESCRIPTION

Bcheck is a wrapper tool for rnpB gene prediction by combining speed of rnabob descriptor model and sensitivity of infernal covariance model.

::DEVELOPER

Ivo Hofacker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Bcheck

:: MORE INFORMATION

Citation

Bcheck: a wrapper tool for detecting RNase P RNA genes
Dilmurat Yusuf, Manja Marz, Peter F Stadler, Ivo L Hofacker
In BMC Genomics, 2010, 11, 1, 432

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