:: DESCRIPTION
RateLimit is a tool to identify rate limiting steps in transcription from RNA production times in live cells.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
TRES is a novel web tool that predicts the likely upstream regulators for a given gene list.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TIPR: transcription initiation pattern recognition on a genome scale.
Morton T, Wong WK, Megraw M.
Bioinformatics. 2015 Aug 8. pii: btv464.
:: DESCRIPTION
EMCMODULE is a program to find regulatory modules using evolutionary Monte Carlo
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: MORE INFORMATION
