> Tag > Links tagged with 'conserved sequence'

Links tagged with 'conserved sequence'

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Found 61 links

Displaying 15 links

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3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures20073
Query3d: a new method for high-throughput analysis of functional residues in protein structures200536
A structural study for the optimisation of functional motifs encoded in protein sequences20047
Three-dimensional profiles: a new tool to identify protein surface similarities199852
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

3MatrixTool Content

http://motif.stanford.edu/distributions/3matrix/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.

This content is being maintained by brutlag.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs200310
NAR Web Server Issue 2003
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tagsamino acid motifs amino acids animals conserved sequence molecular models protein conformation protein databases proteins sequence alignment

3MotifTool Content

http://motif.stanford.edu/distributions/3motif/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.

This content is being maintained by brutlag.

links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database200310
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs200310
NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acids animals conserved sequence database management systems molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment three-dimensional imaging

AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/ [open in a new window]

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DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
AGenDA: gene prediction by cross-species sequence comparison200411
NAR Web Server Issue 2004
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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

ALGGENTool Content

http://alggen.lsi.upc.es/ [open in a new window]

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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.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters200640
FibreHelix, a program for calculating the X-ray diffraction pattern of macromolecules with helical symmetry: application to DNA coiled coils20052
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences20036
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN2003107
PROMO: detection of known transcription regulatory elements using species-tailored searches2002121
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

AREsiteDatabase Content

http://rna.tbi.univie.ac.at/AREsite [open in a new window]

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RNA > Databases

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
AREsite: a database for the comprehensive investigation of AU-rich elements201113
NAR Database Issue 2011
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external linksLink on Wikipedia
tags3' untranslated regions adenine animals base sequence conserved sequence genomics humans mice nucleic acid databases rna sequence analysis rna-binding proteins sequence alignment uracil

Argonne National Laboratory - Computational Biology DatabasesTool Content

http://www-unix.mcs.anl.gov/compbio/index.html [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.

links directory index: 833
TitlePublication YearGoogle Scholar Citation Count
Sentra, a database of signal transduction proteins200216
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction2000369
MPW: the Metabolic Pathways Database1998127
Searching for patterns in genomic data1997221
The metabolic pathway collection from EMP: the enzymes and metabolic pathways database1996100
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tagsanimals bacteria biological transport chemotaxis conserved sequence enzymes eukaryota factual databases fungi genome humans metabolism methylation multigene family open reading frames phosphorylation prokaryotic cells protein databases protein kinases protein-serine-threonine kinases proteins sequence homology signal transduction systems integration tertiary protein structure

BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/ [open in a new window]

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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.

links directory index: 702
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes2001670
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

CDDDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml [open in a new window]

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Protein > Databases

NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships.

This content is being maintained by Aron Marchler-Bauer.

links directory index: 208
TitlePublication YearGoogle Scholar Citation Count
CDD: a Conserved Domain Database for the functional annotation of proteins2011208
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsamino acid sequence biological models conserved sequence protein databases protein sequence analysis proteins tertiary protein structure

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/ [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

links directory index: 3211
TitlePublication YearGoogle Scholar Citation Count
The COG database: new developments in phylogenetic classification of proteins from complete genomes20011177
A genomic perspective on protein families19972034
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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

CompareProspectorTool Content

http://compareprospector.stanford.edu/ [open in a new window]

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

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

links directory index: 164
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
Eukaryotic regulatory element conservation analysis and identification using comparative genomics2004132
NAR Web Server Issue 2004
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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

CONREALTool Content

http://conreal.niob.knaw.nl/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

links directory index: 125
TitlePublication YearGoogle Scholar Citation Count
CONREAL web server: identification and visualization of conserved transcription factor binding sites200541
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting200484
NAR Web Server Issue 2005
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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

ConsiteTool Content

http://www.phylofoot.org/consite/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

links directory index: 514
TitlePublication YearGoogle Scholar Citation Count
ConSite: web-based prediction of regulatory elements using cross-species comparison2004250
Identification of conserved regulatory elements by comparative genome analysis2003264
NAR Web Server Issue 2004
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tagsalgorithms animals binding sites computational biology conserved sequence dna dna footprinting dna sequence analysis genetic models human genome humans nucleic acid regulatory sequences phylogeny predictive value of tests regulator genes sensitivity and specificity sequence alignment transcription factors

CSTminerTool Content

http://www.caspur.it/CSTminer/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences

CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison200427
NAR Web Server Issue 2004
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tagsanimals conserved sequence exons genomics humans intergenic dna mice nucleic acid regulatory sequences sequence tagged sites

EnteriXTool Content

http://enterix.cbcb.umd.edu/ [open in a new window]

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Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

links directory index: 61
TitlePublication YearGoogle Scholar Citation Count
EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae200323
Web-based visualization tools for bacterial genome alignments200038
NAR Web Server Issue 2003
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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella sequence alignment

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