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Links tagged with 'programming languages'

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Found 42 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

BioJavaTool Content

http://www.biojava.org/

Computer Related > Bio-* Programming Tools
Computer Related > Java

The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.

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tagscomputational biology computer systems humans programming languages
setsOpen Bioinformatics Foundation

BioPaxResource Content

http://www.biopax.org/

Computer Related > Bio-* Programming Tools

The BioPAX web site provides information about a collaborative effort to create a data exchange format for biological pathways.

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tagscomputational biology information dissemination metabolic networks and pathways programming languages signal transduction

BioPerlTool Content

http://www.bioperl.org/

Computer Related > Bio-* Programming Tools
Computer Related > PERL

The BioPerl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.

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tagsalgorithms animals biological science disciplines computational biology computer systems database management systems genetic databases humans online systems programming languages software design systems integration
setsOpen Bioinformatics Foundation

BioPythonTool Content

http://biopython.org/

Computer Related > Bio-* Programming Tools

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

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tagscomputational biology computer simulation computer systems database management systems humans macromolecular substances molecular models programming languages protein conformation protein databases
setsOpen Bioinformatics Foundation

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

NAR Web Server Issue 2007
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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

DIALTool Content

http://bioinformatics.bc.edu/clotelab/DIAL/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.

NAR Web Server Issue 2007
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tagsalgorithms base pairing computational biology nucleic acid conformation programming languages protein databases rna rna sequence analysis sequence alignment statistical models

DoelanTool Content

http://www.transcriptome.ens.fr/doelan/

Expression > Transcript Expression Analysis

Doelan is an tool designed to monitor the quality of DNA microarray production.

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tagsalgorithms cluster analysis computational biology computer simulation gene expression profiling oligonucleotide array sequence analysis programming languages sequence alignment

DSHIFTTool Content

http://www.chem.cuhk.edu.hk/DSHIFT/

DNA > Structure and Sequence Feature Detection

DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.

NAR Web Server Issue 2007
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tagsalgorithms base sequence biomolecular nuclear magnetic resonance carbon computational biology computer simulation dna magnetic resonance spectroscopy molecular models molecular sequence data molecular structure nucleic acid conformation oligonucleotides phosphorus programming languages protons reproducibility of results sensitivity and specificity stochastic processes temperature

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

ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

NAR Web Server Issue 2007
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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

EuroPhenomeDatabase Content

http://www.europhenome.org/

Model Organisms > Databases

The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or the predicted phenotype.

NAR Database Issue 2010
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tagsanimals computational biology genetic databases inbred c57bl mice inbred strains mice knockout mice mice phenotype programming languages protein databases tertiary protein structure

FatiGOplusTool Content

http://www.fatigo.org/

DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs animals artificial intelligence binding sites chromosome mapping computational biology dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny programming languages rats sequence alignment systems biology systems integration transcription factors

Gene Set BuilderTool Content

http://www.cisreg.ca/gsb/

DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Human Genome > Other Resources
Model Organisms > General Resources
Protein > Sequence Retrieval

Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access. Gene sets stored in the system can be exported in a variety of output formats - as lists of identifiers, in tables, or as sequences.

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tagscomputational biology database management systems factual databases fungal genes gene expression regulation genetic databases genome genomics humans programming languages