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Links tagged with 'transcription initiation site'

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DBTSSDatabase Content

http://dbtss.hgc.jp/

DNA > Databases

DataBase of Transcription Start Sites (DBTSS) is a database which contains precise positional information for transcription start sites (TSSs) of eukaryotic mRNAs. Included are 330 million new tags generated by massively sequencing the 5'-end of oligo-cap selected cDNAs in humans and mice. 31 different cell types or culture conditions are represented. Differential usage of alternative 5'-ends across cell types and conditions can be viewed in a series of new interfaces. Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated.

This content is being maintained by Kenta Nakai.

NAR Database Issue 2010
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tagsalgorithms animals computational biology gene expression profiling genetic databases genomics humans mice nih 3t3 cells nucleic acid databases protein databases transcription initiation site

EponineTool Content

http://www.sanger.ac.uk/resources/software/eponine/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.

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tagsanimals bayes theorem complementary dna computational biology dna genetic models genetic promoter regions genome human genome humans mice transcription initiation site

Full-parasitesDatabase Content

http://fullmal.hgc.jp/

DNA > Databases
Model Organisms > Databases
RNA > Databases

Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources were interconnected with our original database functionalities. By providing the largest unique full-length cDNA and dynamic transcriptome data, Full-Parasites is useful for understanding host-parasite interactions.

NAR Database Issue 2011
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tagsapicomplexa complementary dna expressed sequence tags gene expression profiling host-parasite interactions humans nucleic acid databases plasmodium falciparum protozoan rna rna sequence analysis toxoplasma transcription initiation site

Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

This content is being maintained by bbth.

NAR Web Server Issue 2003NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence animals bacterial dna bacterial genes bacterial genome bacterial outer membrane proteins base sequence binding sites biological evolution carrier proteins chemical models computational biology consensus sequence dna sequence analysis escherichia coli factual databases gammaproteobacteria gene expression regulation genetic models genetic transcription genetic variation helix-loop-helix motifs homology human genome humans markov chains mice molecular sequence data monte carlo method nonparametric statistics nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology phylogeny protein binding protein prenylation secondary protein structure sequence alignment skeletal muscle statistical models transcription factors transcription initiation site transferases

mGene.webTool Content

http://www.mgene.org/web

DNA > Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources

mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.

NAR Web Server Issue 2009
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tagsalgorithms animals artificial intelligence caenorhabditis caenorhabditis elegans computational biology dna sequence analysis genes genomics helminth genes helminth genome proteins reproducibility of results reverse transcriptase polymerase chain reaction rna splice sites transcription initiation site

PromHTool Content

http://www.softberry.com/berry.phtml?topic=promhg&group=programs&subgroup=promot...

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.

NAR Web Server Issue 2003
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tagsanimals conserved sequence dna sequence analysis genetic promoter regions genomics humans mice nucleic acid regulatory sequences transcription initiation site

PromoSerTool Content

http://biowulf.bu.edu/zlab/PromoSer/

DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection

Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.

NAR Web Server Issue 2004NAR Web Server Issue 2003
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tagsalgorithms animals dna sequence analysis expressed sequence tags genetic promoter regions genome humans messenger rna mice oligonucleotide array sequence analysis rats rna sequence analysis sequence alignment sequence analysis transcription initiation site

RegulonDBDatabase Content

http://regulondb.ccg.unam.mx/

Model Organisms > Databases

RegulonDB is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.

NAR Database Issue 2011
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tagsbacterial gene expression regulation binding sites escherichia coli k12 gene regulatory networks genetic databases genetic transcription signal transduction systems integration transcription factors transcription initiation site

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