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Links tagged with 'response elements'

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AthaMapDatabase Content

http://www.athamap.de/

Expression > Gene Regulation
Model Organisms > Plants

AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

This content is being maintained by Reinhard Hehl.

NAR Web Server Issue 2005
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tagsarabidopsis arabidopsis proteins base sequence binding sites cold temperature computational biology conserved sequence dehydration genetic databases genetic transcription genomics molecular sequence data nucleic acid databases plant dna plant gene expression regulation plant genes plant genome protein binding response elements sequence alignment systems integration transcription factors transcriptional regulatory elements untranslated rna

CisMolsTool Content

http://cismols.cchmc.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Comparative Genomics

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

NAR Web Server Issue 2005
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tagsbase sequence binding sites conserved sequence gene expression regulation genomics response elements transcription factors

cisREDDatabase Content

http://www.cisred.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

cisRED is a database system for genome-scale computational discovery of regulatory elements.

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tagsanimals computational biology genetic promoter regions genomics nucleic acid databases response elements

ERPINTool Content

http://tagc.univ-mrs.fr/erpin/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

NAR Web Server Issue 2004
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tagsalgorithms base sequence computational biology conserved sequence gene expression regulation iron nucleic acid conformation nucleic acid sequence homology response elements ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis selenocysteine sensitivity and specificity sequence alignment transfer rna

JASPARTool Content

http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.

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tagsanimals base sequence binding sites computational biology dna eukaryotic cells genetic transcription humans molecular sequence data nucleic acid databases response elements transcription factors

jPREdictorTool Content

http://bibiserv.techfak.uni-bielefeld.de/jpredictor/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.

NAR Web Server Issue 2006
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tagsanimals binding sites drosophila melanogaster drosophila proteins genomics response elements transcription factors transcriptional regulatory elements

MADAPTool Content

http://ccg.vital-it.ch/madap/

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

NAR Web Server Issue 2007
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tagsalgorithms animals base sequence chromatin immunoprecipitation cluster analysis complementary dna computational biology dna primers eukaryotic cells expressed sequence tags genetic databases genetic promoter regions genome humans nucleic acid databases open reading frames response elements statistical models

MDscanTool Content

http://robotics.stanford.edu/~xsliu/MDscan/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

This content is being maintained by brutlag.

NAR Web Server Issue 2004
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tagsalgorithms base sequence binding sites chromatin computational biology dna dna-binding proteins fungal genes gene expression regulation genetic transcription nucleic acid regulatory sequences oligonucleotide array sequence analysis precipitin tests protein binding response elements saccharomyces cerevisiae saccharomyces cerevisiae proteins sensitivity and specificity telomere telomere-binding proteins time factors transcription factors

OSU Bioinformatics and Computational BiologyResource Content

http://www.cancergenetics.med.ohio-state.edu/

DNA > DNA and Genomic Analysis
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

The website of the Ohio State University Human Cancer Genetics Bioinformatics group. This site has many resources, including databases of promoters and transcription factors, software tools to predict potential P53 consensus binding sites and to predict first exon and promoter regions and a software toolkit for developing web-based applications to view genomic data.

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tagsanimals computational biology erythrocytes exons gene expression profiling genetic promoter regions genetic transcription hematopoiesis humans mice nucleic acid databases response elements

rMotifTool Content

http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Yeast

rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).

NAR Web Server Issue 2003
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tagsdna sequence analysis genetic promoter regions genetic transcription messenger rna nucleic acid regulatory sequences response elements

SCOPETool Content

http://genie.dartmouth.edu/scope/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE does not have any nuisance parameters so does not require the user to guess what the results might be. SCOPE is also very robust to noisy data and is still 50% as accurate even in the presence of 4-fold noise. SCOPE can also identify other genes in the genome that might be coregulated with the original gene set.

This content is being maintained by bobgross.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence homology artificial intelligence automated pattern recognition base sequence binding sites cluster analysis computational biology computer simulation consensus sequence conserved sequence dna dna sequence analysis gene expression profiling gene expression regulation genetic models genetic promoter regions molecular sequence data oligonucleotide array sequence analysis predictive value of tests protein binding proteins response elements saccharomyces cerevisiae sequence alignment statistical models transcription factors transcriptional regulatory elements

SSATool Content

http://www.isrec.isb-sib.ch/ssa/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).

NAR Web Server Issue 2003
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tagsbacterial genome consensus sequence dna sequence analysis genetic promoter regions nucleic acid regulatory sequences protein biosynthesis response elements ribosomal rna transcription initiation site

SynoRTool Content

http://synor.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SynoR searches vertebrate genomes for synonymous regulatory elements.

NAR Web Server Issue 2005
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tagsanimals binding sites cardiac myocytes gene expression regulation genomics humans mice rats response elements transcription factors vertebrates