:: DESCRIPTION
ConSite explores transcription factor binding sites shared by two genomic sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52.
ConSite: web-based prediction of regulatory elements using cross-species comparison.
Sandelin A, Wasserman WW, Lenhard B.
:: DESCRIPTION
FOOTER analyses a pair of homologous mammalian DNA sequences (i.e. human and mouse/rat) for high probability binding sites of known transcription factors. A set of Position-Specific Scoring Matrices (PSSM) has been carefully constructed from mammalian transcription factor binding sites deposited in TRANSFAC database.
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.
Corcoran DL, Feingold E, Benos PV.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.
:: DESCRIPTION
TOBIAS is a framework of tools for investigating transcription factor binding from ATAC-seq signal
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
Mette Bentsen, et al.
doi: https://doi.org/10.1101/869560
:: DESCRIPTION
BaalChIP ( Bayesian Analysis of Allelic imbalances from ChIP-seq data) corrects for the effect of background allele frequency on the observed ChIP-seq read counts jointly analyses multiple ChIP-seq samples across a single variant.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol, 18 (1), 39 2017 Feb 24
BaalChIP: A probabilistic framework for reconstructing intra-tumor phylogenies
I. de Santiago, W. Liu, K. Yuan, M. O’Reilly, CS. Chilamakuri, B. Ponder, K. Meyer, F. Markowetz
:: DESCRIPTION
ChIPModule is a software tool for systematical discoveray of transcription factors and their cofactors from ChIP-seq data. Given a ChIP-seq dataset and motifs of a large number of transcription factors, ChIPModule can efficiently identify groups of motifs,whose instances significantly co-occur in the ChIP-seq peak regions.
::DEVELOPER
Hu Lab – Data Integration and Knowledge Discovery @ UCF
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Pac Symp Biocomput. 2013:320-31.
ChIPModule: systematic discovery of transcription factors and their cofactors from ChIP-seq data.
Ding J, Cai X, Wang Y, Hu H, Li X.
:: DESCRIPTION
activeTF is to find a set of coordinately activated Transcription Factors (TF) from a given gene expression dataset.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genomics. 2010 Mar;95(3):143-50. doi: 10.1016/j.ygeno.2009.12.006. Epub 2010 Jan 6.
An efficient algorithm to identify coordinately activated transcription factors.
Hu H.
:: DESCRIPTION
TFBS Evo is a model which traces the evolution of lineage-specific transcription factor binding sites without relying on detailed base-by-base cross-species alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.
Yokoyama KD, Zhang Y, Ma J.
PLoS Comput Biol. 2014 Aug 21;10(8):e1003771. doi: 10.1371/journal.pcbi.1003771.
:: DESCRIPTION
TFBIND is a software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)).
::DEVELOPER
Laboratory for Medical Science Mathematics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 1999 Jul-Aug;15(7-8):622-30.
Estimating transcription factor bindability on DNA.
Tsunoda T, Takagi T.
:: DESCRIPTION
ZifNet is the package that can be used to predict the DNA binding model for any given a C2H2 zinc finger based on back-propagation algorithm. It includes two parts: First, identify the optimal DNA-zinc finger interaction model with the core C programs of ZifNet. And second, predict DNA-binding weight matrix models for Zinc fingers using the auxiliary codes, and the defined DNA-zinc finger interaction model derived from the last step.
::DEVELOPER
Stormo Lab in Department of Genetics, Washington University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
DME (Discriminating Motif Enumerator) is a program that discovers transcription factor binding site motifs in nucleotide sequences. DME identifies motifs, represented as position weight matrices, that are overrepresented in one set of sequences relative to another set. The ability to directly optimize relative overrepresentation is a unique feature of DME, making DME an ideal tool for analyzing promoters of transcripts found to have differential expression in a particular context. The optimization procedure is based on an enumerative algorithm that is guaranteed to identify optimal motifs from a discrete space of matrices with a specific lower bound on information content. This strategy scales very well with the number and length of the sequences used, and is well-suited to analyzing very large data sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
MORE INFORMATION
Citation
Bioinformatics. 2007 Jan 1;23(1):21-9. Epub 2006 Oct 18.
Computational prediction of novel components of lung transcriptional networks.
Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS.
