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Regulation of Transcription
Databases & Resources
List of Transcriptional regulator sites and transcription factors Databases at Nucleic Acid Research.
TRANSFAC contains data on transcription factors, their experimentelly-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices.
PathoDB 2.0 Public 2005 is a database on pathologically relevant mutated forms of transcription factors and their binding sites.
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
ChlamyTFDB (1.0) is a public database arising from efforts to identify and catalogue all Chlamydomonas reinhardtii genes involved in transcriptional control.
PlnTFDB (3.0) is a public database arising from efforts to identify and catalogue all Plant genes involved in transcriptional control.
Over-represented Transcription Factor Binding Site Prediction Tool is a method base on TRANSFAC Matrix, it can detect over-represented motifs of known transcription factors from a set of related sequences. Particularly, promoters of a same gene family or from the same tissue can be submitted as a analysis subject. Promoters of putative co-regulated genes clustered with gene expression data should be also a good candidate to analysis.
The high-quality transcription factor binding profile database
Promoters
Compares two DNA sequences assuming colinear blocks, ideal for promoters.
Compares two DNA sequences allowing for inversions and translocations, ideal for promoters.
An online tool using Neural Network Promoter Prediction version 2.2
Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.
Promoter2.0 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.
Analysis of the promoter sequence of genes using TF-maps (maps of predicted transcription factors)
Promoter region analysis by alignment of TF-maps (maps of predicted transcription factors)
PlantProm DB is an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species.
PromEC is an updated compilation of E. coli mRNA promoter sequences.
Ribosome Binding Sites
The Ribosome Binding Site (RBS) Calculator is a design method for predicting and controlling translation initiation and protein expression in bacteria. The method can predict the rate of translation initiation for every start codon in an mRNA transcript. The method may also optimize a synthetic RBS sequence to achieve a targeted translation initiation rate. Using the RBS Calculator, a protein coding sequence's translation rate may be rationally controlled across a 100,000+ fold range.
Transcription Factor Binding Sites
TESS is a web tool for predicting transcription factor binding sites in DNA sequences.
TFM (Transcription Factor Matrices) is a software suite for identifying and analyzing transcription factor binding sites in DNA sequences.
Regulatory VISTA combines transcription factor binding sites database search with a comparative sequence analysis. It can be used directly or through mVISTA, Genome VISTA, or VISTA Browser.
Online tool to detect and visualize compositionally similar cis-element clusters in the context of conserved sequences. Within a high-scoring region, the relative arrangement of shared cis-elements within compositionally similar TF-binding site clusters is depicted in a Trafacgram.
Phylogenetic footprinting is a method that identifies putative regulatory elements in DNA sequences. FootPrinter identifies regions of DNA that are unusually well conserved across a set of orthologous sequences.
TFM-Explorer (Transcription Factor Matrix Explorer) is a program for analysing regulatory regions of eukaryotic genomes.
This web application allows you to compare a set of position weight matrices (PWM) against the T-Reg database! T-Reg is a relational database on transcriptional regulation that contains a collection of PWMs.
SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences.
EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data. It is capable of (1) clustering (2) visualizing (3) biclustering and (4) performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis. In particular, it can analyze groups of genes for enrichment of transcription factor binding sites in their promoters.
Over-represented Transcription Factor Binding Site Prediction Tool.
Transcription Terminators
TransTermHP finds rho-independent transcription terminators in bacterial genomes.
CpG Islands
CpG Islands searches for CpG islands in a DNA sequence using the method described by Gardiner-Garden and Frommer (1987).
The CpG island searcher screens for CpG islands which meet the criteria selected below in submitted DNA sequences.
CpG Island finder and plotting tool. An EMBOSS tool at the EBI that detects regions of genomic sequences rich in the CpG pattern.
GrailEXP is a software package that predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence.
GC Content
Calculates fractional GC content of nucleic acid sequences
The Web Bench
The Web Bench
is the essential companion to the biologist, bringing informational resources and a collection of tools & calculators to facilitate work at the bench and analysis of biological data.
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Sequence Analysis with GenBeans
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