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.

PASTAA – Detecting Transcriptions Factors Associated with Functional Categories

PASTAA

:: DESCRIPTION

PASTAA is a software for detecting transcriptions factors associated with functional categories, which utilizes the prediction of binding affinities of a TF to promoters. This binding strength information is compared to the likelihood of membership of the corresponding genes in the functional category under study. Coherence between the two ranked datasets is seen as an indicator of association between a TF and the category. PASTAA is applied primarily to the determination of TFs driving tissue-specific expression.

::DEVELOPER

the Computational Molecular Biology Department at the Max Planck Institute for Molecular Genetics in Berlin, Germany.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 PASTAA

:: MORE INFORMATION

Citation

Helge G. Roider*, Thomas Manke, Sean O’Keeffe, Martin Vingron and Stefan A. Haas
PASTAA: identifying transcription factors associated with sets of co-regulated genes
Bioinformatics (2009) 25 (4): 435-442.

Pscan-ChIP 1.3 – Finding Over-represented Transcription Factor-binding Site Motifs

Pscan-ChIP 1.3

:: DESCRIPTION

PscanChIP is a web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria.

::DEVELOPER

Bioinformatics Evolution @nd COmparative geNomics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PscanChIP

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.
PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Zambelli F1, Pesole G, Pavesi G.

coMotif 1.0 – Identify Transcription Co-regulator Binding Sites in ChIP-seq Data

coMotif 1.0

:: DESCRIPTION

coMotif is a software of three-component mixture framework to model the joint distribution of two motifs as well as the situation where some sequences contain only one or none of the motifs.

::DEVELOPER

coMotif team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 coMotif 

:: MORE INFORMATION

Citation:

Mengyuan Xu, Clarice R. Weinberg, David M. Umbach and Leping Li
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
Bioinformatics (2011) 27 (19): 2625-2632.

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.

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.

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.

TargetOrtho – A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets

TargetOrtho

:: 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.