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NAR Web Server Issue 2003

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Found 106 links

Displaying 15 links

3MatrixTool Content

http://motif.stanford.edu/distributions/3matrix/

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.

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/

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.

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

AHMIITool Content

http://www.wdcm.org/AHMII/ahmii.html

Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Yeast

Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

NAR Web Server Issue 2003
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tagsbacteria cell line fungi microbiological techniques reproducibility of results systems integration yeasts

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

AMIGeneTool Content

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

DNA > Gene Prediction
Model Organisms > Microbes

Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genes dna sequence analysis markov chains open reading frames

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

Bioinformatics Links DirectoryResource Content

http://www.bioinformatics.ca/links_directory/

Education > Directories and Portals

The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.

This content is being maintained by Francis Ouellette.

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external linksLink on TwitterLink on Wikipedia
tagscomputational biology directories as topic factual databases genetic databases genetics humans molecular biology
setsOntario Institute for Cancer Research (OICR)

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

BLAST2SRSTool Content

http://blast2srs.embl.de/

Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.

NAR Web Server Issue 2003
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tagsamino acid sequence homology animals humans protein databases

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

ChipInfoTool Content

http://genomics.bioen.illinois.edu/chipinfo/

Expression > Transcript Expression Analysis

ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.

NAR Web Server Issue 2003
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tagsdna probes gene expression profiling genetic databases oligonucleotide array sequence analysis systems integration

ClustalWTool Content

http://www.ebi.ac.uk/clustalw/

Sequence Comparison > Multiple Sequence Alignments

Standard multiple sequence alignment.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence globins molecular sequence data nucleic acids phylogeny protein sequence analysis proteins secondary protein structure sensitivity and specificity sequence alignment sequence analysis

Cluster BusterTool Content

http://zlab.bu.edu/cluster-buster/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.

NAR Web Server Issue 2003
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tagsbinding sites cluster analysis dna sequence analysis genetic code humans nucleic acid regulatory sequences transcription factors

CODEHOPTool Content

http://blocks.fhcrc.org/codehop.html

DNA > Tools For the Bench

COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.

NAR Web Server Issue 2003
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tagsamino acid sequence base sequence consensus sequence dna primers oligonucleotides polymerase chain reaction protein sequence analysis sequence alignment

CRPDatabase Content

http://fasta.bioch.virginia.edu/crp/

Protein > Domains and Motifs
Protein > Sequence Features

Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.

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tagsamino acid sequence biochemistry dna sequence analysis humans molecular sequence data neoplasm proteins neural networks (computer) phosphoproteins phosphorylation phosphoserine phosphothreonine phosphotyrosine protein sequence analysis proteins radioactive tracers recombinant proteins sensitivity and specificity