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Links tagged with 'automation'

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Found 22 links

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3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

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.

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

AsteriasTool Content

http://asterias.bioinfo.cnio.es/

DNA > Annotations
Expression > Transcript Expression Analysis

Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.

This content is being maintained by rdiaz02.

NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition automation cluster analysis computational biology computer simulation database management systems dna sequence analysis gene expression profiling genetic models genomics humans nucleic acid hybridization oligonucleotide array sequence analysis programming languages sequence alignment statistical models

CATHDatabase Content

http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).

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tagsamino acid sequence homology animals automation genomics protein databases protein folding protein structural homology proteins secondary protein structure tertiary protein structure

EMAGEDatabase Content

http://www.emouseatlas.org/emage/

Expression > Databases
Model Organisms > Databases

EMAGE is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.

NAR Database Issue 2010
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tagsanimals automation computational biology database management systems developmental gene expression regulation embryonic development factual databases gene expression gene expression profiling genetic databases mammalian embryo mice molecular imaging nucleic acid databases programming languages

EVATool Content

http://cubic.bioc.columbia.edu/eva/

Computer Related > Math and Statistics
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.

NAR Web Server Issue 2003
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tagsautomation protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins reproducibility of results secondary protein structure sequence alignment

GenePublisherTool Content

http://www.cbs.dtu.dk/services/GenePublisher

Expression > Transcript Expression Analysis

GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.

NAR Web Server Issue 2003
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tagsautomation cluster analysis gene expression profiling genetic databases genetic promoter regions metabolism nucleic acid regulatory sequences oligonucleotide array sequence analysis signal transduction

GRAMM-XTool Content

http://vakser.bioinformatics.ku.edu/resources/gramm/grammx

Protein > Molecular Dynamics and Docking

GRAMM-X is a protein docking server.

NAR Web Server Issue 2006
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tagsalgorithms antigen-antibody complex automation binding sites computational biology computer simulation dimerization evaluation studies as topic influenza virus hemagglutinin glycoproteins ligands macromolecular substances molecular conformation molecular models multiprotein complexes protein conformation protein databases protein folding protein interaction mapping protein structural homology proteomics reproducibility of results statistical models tertiary protein structure viral antibodies

KAASTool Content

http://www.genome.jp/kegg/kaas/

DNA > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

NAR Web Server Issue 2007
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tagsanimals artificial intelligence automation chromosome mapping computational biology controlled vocabulary database management systems documentation genome humans proteome sequence analysis signal transduction

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MousebookDatabase Content

http://www.mousebook.org/

Model Organisms > Databases

The MouseBook databases and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. The MouseBook portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide value-added information. MouseBook can be searched either using an intuitive Google style free text search or using the Mammalian Phenotype (MP) ontology tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database.

NAR Database Issue 2010
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tagsalleles animals automation computational biology cryopreservation genetic databases mice mutation nucleic acid databases phenotype

NTMGTool Content

http://oblab.cs.nchu.edu.tw:8080/WebSDL/

DNA > Tools For the Bench

NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.

NAR Web Server Issue 2007
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tagsalgorithms automation complementary dna dna primers dna sequence analysis gene deletion humans mutagenesis mutation polymerase chain reaction single nucleotide polymorphism

One-Block CYRCATool Content

http://bioinformatics.weizmann.ac.il/~milana/OneCYRCA/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

One-Block CYRCA is a program for identifying blocks (local ungapped profiles of the most conserved regions of protein families and domains) in a multiple sequence alignment based on the LAMA and CYRCA block-to-block alignment methods.

NAR Web Server Issue 2005
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tagsadenosine triphosphatases algorithms amino acid motifs amino acid sequence amino acid sequence homology aspartylglucosylaminase automation binding sites catalysis computational biology conserved sequence dna nucleotidyltransferases dna-binding proteins endopeptidase clp enoyl-coa hydratase factual databases flavin-adenine dinucleotide gamma-glutamyltransferase helix-turn-helix motifs hydrolysis ligands molecular models protein binding protein databases protein folding protein sequence analysis proteins sequence alignment serine endopeptidases single-stranded dna structure-activity relationship tertiary protein structure transposases

Pcons.netTool Content

http://pcons.net/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence animals automatic data processing automation computational biology computer simulation consensus sequence humans molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins roc curve secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

PolyPhredTool Content

http://droog.gs.washington.edu/polyphred/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

UNIX-based tool for sequence trace based genotyping; integrated with Phred/Phrap/Consed (see DNA -- Contig Assembly); free for non-commercial use.

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tagsanimals antigen receptors automation base sequence dna dna sequence analysis fluorescence genotype humans molecular sequence data

Primer ZTool Content

http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do

DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat

Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.

NAR Web Server Issue 2007
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tagsalgorithms automation computational biology dna primers exons genetic databases genetic promoter regions genetic techniques humans messenger rna polymerase chain reaction single nucleotide polymorphism