Promoter 2.0 – Transcription Start Sites in Vertebrate DNA

Promoter 2.0

:: DESCRIPTION

Promoter predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions. It builds on principles that are common to neural networks and genetic algorithms.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Promoter

:: MORE INFORMATION

Citation

Promoter 2.0: for the recognition of PolII promoter sequences.
Steen Knudsen
Bioinformatics 15, 356-361, 1999.

TSSi 1.16.0 – Transcription Start Site Identification

TSSi 1.16.0

:: DESCRIPTION

The TSSi package identifies and normalizes transcription start sites in high-throughput sequencing data.

::DEVELOPER

Julian Gehring, Clemens Kreutz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

 TSSi

:: MORE INFORMATION

Citation:

TSSi–an R package for transcription start site identification from 5′ mRNA tag data.
Kreutz C, Gehring JS, Lang D, Reski R, Timmer J, Rensing SA.
Bioinformatics. 2012 Jun 15;28(12):1641-2. doi: 10.1093/bioinformatics/bts189.

TSSAR 1.0.1 – Transcription Start Site Annotation Regime

TSSAR 1.0.1

:: DESCRIPTION

TSSAR is a Web Service for predicting bacterial Transcription Start Sites from dRNA-seq data. It is built on a RESTful Client/Server architecture that allows for rapid screening and processing of Next-Generation Sequencing data.

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX/ Windows
  • Java
  • R package

:: DOWNLOAD

 TSSAR

 :: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Mar 27;15:89. doi: 10.1186/1471-2105-15-89.
TSSAR: TSS annotation regime for dRNA-seq data.
Amman F1, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF,Findeiß S.

GS-Finder 1.4 – Find Bacterial Gene Start Sites

GS-Finder 1.4

:: DESCRIPTION

GS-Finder is a program to find bacterial gene start sites with a self-training method.

::DEVELOPER

TUBIC – the Tianjin University BioInformatics Centre.

:: REQUIREMENTS

  • Windows / Linux / SGI IRIX

:: DOWNLOAD

  GS-Finder

:: MORE INFORMATION

Citation

H.Y Ou, F.B. Guo and C.T. Zhang (2004).
GS-Finder: a program to find bacterial gene start sites with a self-training method.
Int. J. Biochem. Cell Biol. 36, 535-544.