> > Structure and Sequence Feature Detection

Structure and Sequence Feature Detection

This section contains links to tools for DNA structure prediction and finding regulatory sequences, the base composition, binding sites and motifs in your sequence of interest.

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Found 145 links

Displaying 15 links

3D-DARTTool Content

http://haddock.chem.uu.nl/dna/

DNA > Structure and Sequence Feature Detection

The 3D-DART web server interfaces to a collection of tools for the generation of DNA structural models in custom conformations.

This content is being maintained by mvdijk.

NAR Web Server Issue 2009
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tagsdna molecular models nucleic acid conformation

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

AlignACETool Content

http://arep.med.harvard.edu/mrnadata/mrnasoft.html

DNA > Structure and Sequence Feature Detection

Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement.

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ARGOTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

NAR Web Server Issue 2005
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tagsalgorithms binding sites eukaryotic cells gene expression regulation genetic promoter regions genomics transcription factors

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

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

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

NAR Web Server Issue 2004
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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

BioBayesNetTool Content

http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Sequence Features

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence automated pattern recognition bayes theorem binding sites chemical models computational biology computer simulation dna sequence analysis genetic models molecular models molecular sequence data protein binding protein conformation protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship transcription factors

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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BioMartTool Content

http://biomart.org

DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
RNA > Databases

BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).

NAR Web Server Issue 2009
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tagsbiology genetic databases
setsBioMart Ontario Institute for Cancer Research (OICR)

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

NAR Web Server Issue 2008
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tagsalgorithms cluster analysis computational biology gene expression profiling

BioProspectorTool Content

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

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

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

CEASTool Content

http://ceas.cbi.pku.edu.cn

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

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

NAR Web Server Issue 2006
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tagsbinding sites chromatin immunoprecipitation genomics human genome humans oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

NAR Web Server Issue 2008
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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

ChinookTool Content

http://www.bcgsc.bc.ca/chinook/

Computer Related > Web Services
DNA > DNA and Genomic Analysis
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.

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tagsbenchmarking biomedical technology assessment computational biology computing methodologies software validation

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

Tags associated with subcategory 'DNA/Structure and Sequence Feature Detection'

dna sequence analysis binding sites transcription factors algorithms humans animals computational biology genetic promoter regions sequence alignment genomics nucleic acid regulatory sequences dna base sequence gene expression regulation mice molecular sequence data nucleic acid databases conserved sequence gene expression profiling human genome genetic databases genetic transcription saccharomyces cerevisiae serine endopeptidases gene expression regulon histones prokaryotic cells transcriptional regulatory elements tetraodontiformes leghemoglobin initiator codon anti-infective agents operon proteome biomedical engineering archaeal genes chemical dictionaries evaluation studies as topic archaeal genome mycobacterium tuberculosis nucleosomes cluster analysis predictive value of tests physicochemical phenomena peptides physical chemistry dna-binding proteins open reading frames muscles liver e2f transcription factors database management systems neural networks (computer) likelihood functions response elements cultured cells culture techniques amino acid motifs statistical data interpretation rna drosophila probability rna splicing sequence homology expressed sequence tags rna precursors breast neoplasms biomedical technology assessment recombinant proteins pseudomonas aeruginosa drosophila melanogaster equipment failure analysis neoplastic gene expression regulation neoplasms multigene family female plant dna complementary dna nucleic acid probes x-ray crystallography horizontal gene transfer bacteria cardiac myocytes up-regulation mammals dna footprinting terminology as topic vertebrates programming languages hypercholesterolemia telomere ubiquitin saccharomyces cerevisiae proteins precipitin tests telomere-binding proteins hypoxanthine phosphoribosyltransferase ribonucleic acid regulatory sequences point mutation oligonucleotides introns