RateLimit – Rate Limiting Steps in Transcription from RNA production times in live cells

RateLimit

:: DESCRIPTION

RateLimit is a tool to identify rate limiting steps in transcription from RNA production times in live cells.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

RateLimit

:: MORE INFORMATION

Citation:

Häkkinen A, Ribeiro AS.
Characterizing rate limiting steps in transcription from RNA production times in live cells.
Bioinformatics. 2016 May 1;32(9):1346-52. doi: 10.1093/bioinformatics/btv744. Epub 2015 Dec 31. PMID: 26722120.

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.

TRES – Transcription Regulation in Embryonic Stem Cell

TRES

:: DESCRIPTION

TRES is a novel web tool that predicts the likely upstream regulators for a given gene list.

::DEVELOPER

The Roslin Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TRES predicts transcription control in embryonic stem cells.
Pooley C, Ruau D, Lombard P, Gottgens B, Joshi A.
Bioinformatics. 2014 Jun 23. pii: btu399.

Parseq rev02 – Infer Transcription level from RNA-Seq Read Counts

Parseq rev02

:: DESCRIPTION

Parseq is a statistical approach for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts.

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Parseq

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1409-16. doi: 10.1093/bioinformatics/btu042. Epub 2014 Jan 27.
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models.
Mirauta B1, Nicolas P, Richard H.

TargetOrtho 2.0 – A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets

TargetOrtho 2.0

:: DESCRIPTION

TargetOrtho provides a cost- and time-efficient in silico approach for the identification of novel TF target genes, and, together with its CRM search function, is poised to unravel the regulatory logic of diverse biological processes.

::DEVELOPER

Hobert Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 TargetOrtho

:: MORE INFORMATION

Citation

Genetics. 2014 May;197(1):61-76. doi: 10.1534/genetics.113.160721. Epub 2014 Feb 20.
TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets.
Glenwinkel L1, Wu D, Minevich G, Hobert O.

CapFilter – Analysis tool for Identifying high Confidence Transcription Start Sites

CapFilter

:: DESCRIPTION

CapFilter is a straightforward annotation-agnostic computational pipeline that greatly increases confidence in predicted TSSs and allows tuning by the end-user to balance both precision and sensitivity of TSS identification to address experimental needs.

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CapFilter

:: MORE INFORMATION

Citation

Jason S. Cumbie, Maria G. Ivanchenko, and Molly Megraw. (2015).
NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.
BMC Genomics, 16:597. doi:10.1186/s12864-015-1670-6

3PEAT – Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

3PEAT

:: DESCRIPTION

3PEAT (Plant PEAT Peaks) predicts the probability of a TSS at any given nucleotide in the Arabidopsis genome solely from the DNA sequence surrounding that nucleotide.

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 3PEAT

:: MORE INFORMATION

Citation

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. (2014).
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Plant Cell, 26:2746-60.

TIPR – Transcription Initiation Pattern Recognition on a Genome Scale

TIPR

:: DESCRIPTION

TIPR (Transcription Initiation Pattern Recognizer) is a sequence-based machine learning model that identifies TSSs with high accuracy and resolution for multiple spatial distribution patterns along the genome, including broadly distributed TSS patterns that have previously been difficult to characterize.

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TIPR

:: MORE INFORMATION

Citation

TIPR: transcription initiation pattern recognition on a genome scale.
Morton T, Wong WK, Megraw M.
Bioinformatics. 2015 Aug 8. pii: btv464.

EMCmodule 0.1 – Discovery of Transcription Regulatory Modules using Evolutionary Monte Carlo

EMCmodule 0.1

:: DESCRIPTION

EMCMODULE is a program to find regulatory modules using evolutionary Monte Carlo

::DEVELOPER

Mayetri Gupta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EMCmodule

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2005 May 17;102(20):7079-84.
De novo cis-regulatory module elicitation for eukaryotic genomes.
Gupta M, Liu JS.

MultiTF-PPI – Competitive Transcription Factor Binding Prediction

MultiTF-PPI

:: DESCRIPTION

MultiTF-PPI is a probabilistic protein-protein interaction guided method for competitive transcription factor binding prediction.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Matlab

:: DOWNLOAD

MultiTF-PPI

:: MORE INFORMATION