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Links tagged with 'user-computer interface'

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Found 30 links

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ChimerDBDatabase Content

http://ercsb.ewha.ac.kr/fusiongene [open in a new window]

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DNA > Databases

ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChimerDB 2.0--a knowledgebase for fusion genes updated20106
NAR Database Issue 2010
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tagsalgorithms animals chromosomes computational biology expressed sequence tags gene expression profiling gene fusion genetic databases genetic translocation genomics humans information storage and retrieval internet messenger rna mice mutant chimeric proteins nucleic acid databases protein databases pubmed rats software user-computer interface

ELMTool Content

http://elm.eu.org/ [open in a new window]

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Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

links directory index: 1035
TitlePublication YearGoogle Scholar Citation Count
ELM--the database of eukaryotic linear motifs201215
ELM: the status of the 2010 eukaryotic linear motif resource201090
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
NAR Database Issue 2010NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology computer graphics disease eukaryota eukaryotic cells genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins software tertiary protein structure user-computer interface viral proteins

EMAGEDatabase Content

http://www.emouseatlas.org/emage/ [open in a new window]

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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.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
The BioMart interface to the eMouseAtlas gene expression database EMAGE20112
EMAGE mouse embryo spatial gene expression database: 2010 update201028
NAR Database Issue 2010
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tagsaccess to information animals automation computational biology database management systems developmental gene expression regulation embryonic development factual databases gene expression gene expression profiling genetic databases immunohistochemistry in situ hybridization information storage and retrieval internet mammalian embryo messenger rna mice molecular imaging nucleic acid databases programming languages proteins reporter genes software user-computer interface

ePMVTool Content

http://epmv.scripps.edu/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

We have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (blender,maya and cinema4D) to provide simultaneous access the capabilities of all of the systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease.

This content is being maintained by ludovicautin.

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TitlePublication YearGoogle Scholar Citation Count
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tags3D algorithms animals blender cinema4d computational biology computer graphics electrocardiography female fetal heart fetal monitoring fetus heart rate humans interdisciplinary communication maya mice modelling molecular biology molecular conformation molecular dynamics simulation molecular graphism molecular models motion movement phtorealistic pregnancy prospective studies rem sleep rendering software three-dimensional imaging user-computer interface vizualisation

ExPASy Molecular Biology ServerResource Content

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

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Education > Directories and Portals
Protein > Do-it-all Tools for Protein

ExPASy is the bioinformatics resource portal for access to programs and databases for the analysis of proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

links directory index: 1342
TitlePublication YearGoogle Scholar Citation Count
ExPASy: The proteomics server for in-depth protein knowledge and analysis20031342
NAR Web Server Issue 2003NAR Web Server Issue 2012
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tagsenzymes gel electrophoresis internet molecular models protein conformation protein databases protein sequence analysis proteins proteomics software systems integration user-computer interface

Filamentous Fungal Gene Expression Database (FFGED)Database Content

http://bioinfo.townsend.yale.edu/ [open in a new window]

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Expression > Databases
Model Organisms > Databases

The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.

This content is being maintained by Jeffrey P. Townsend.

links directory index: 158
TitlePublication YearGoogle Scholar Citation Count
Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons200741
Enabling a community to dissect an organism: overview of the Neurospora functional genomics project200764
Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination200553
NAR Web Server Issue 2005
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tagsalgorithms amitrole animals base sequence basic-leucine zipper transcription factors bayes theorem ChIP-seq chromosome mapping cluster analysis computational biology computer graphics database management systems dictyostelium dna-binding proteins enzyme inhibitors experimental design expressed sequence tags fungal dna fungal gene expression regulation fungal genes fungal genome fungal proteins fungal spores gene deletion gene expression gene expression profiling gene library genetic databases genetic models genetic promoter regions genetic techniques genetic transcription genomics internet messenger rna microarray molecular sequence data mutation neurospora neurospora crassa northern blotting nucleic acid databases oligonucleotide array sequence analysis oligonucleotide probes phenotype regulon related experiments reproducibility of results rna-seq saccharomyces cerevisiae saccharomyces cerevisiae proteins sequence alignment single nucleotide polymorphism software statistical models systems integration transcription factors user-computer interface ustilago

GeneCardsDatabase Content

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

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Human Genome > Health and Disease

Database of human genes, their products, and involvement in diseases; free for non-commercial use, but users should also read the Terms of Use for this site.

links directory index: 124
TitlePublication YearGoogle Scholar Citation Count
GeneCards: integrating information about genes, proteins and diseases1997124
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tagsalgorithms chromosome mapping computer communication networks database management systems factual databases gene expression profiling genetic databases human genome human genome project humans information storage and retrieval internet medical genetics sequence alignment sequence analysis software user-computer interface

genenames.orgDatabase Content

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

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Literature > Databases

genenames.org displays all approved nomenclature within Symbol Reports that contain data curated by HUGO Gene Nomenclature Committee (HGNC) editors and links to related genomic, phenotypic and proteomic information. New features include a new Quick Gene Search, a new List Search, an integrated HGNC BioMart and a new Statistics and Downloads facility.

This content is being maintained by HGNC.

links directory index: 296
TitlePublication YearGoogle Scholar Citation Count
genenames.org: the HGNC resources in 2011201136
The HGNC Database in 2008: a resource for the human genome2008125
Genew: the Human Gene Nomenclature Database, 2004 updates2004135
NAR Database Issue 2011
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tagsanimals computational biology gene symbols genes genetic databases genetic variation genomics human genome humans information storage and retrieval internet mice nomenclature phenotype proteomics software systems integration terminology as topic user-computer interface

GOLDDatabase Content

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

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DNA > Databases
Model Organisms > Databases
Model Organisms > General Resources

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. GOLD is in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification.

links directory index: 239
TitlePublication YearGoogle Scholar Citation Count
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata20128
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata2010231
NAR Database Issue 2010
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tags20th century history 21st century history animals archaeal genome bacterial genome computational biology environmental microbiology factual databases genetic databases genome genomics human genome project humans information storage and retrieval international cooperation internet metagenomics nucleic acid databases online systems phylogeny protein databases software systems integration tertiary protein structure user-computer interface

HMDBDatabase Content

http://www.hmdb.ca/ [open in a new window]

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Human Genome > Other Resources
Other Molecules > Metabolites

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
Metabolomics: the principles and potential applications to transplantation200573
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tagsbiochemical phenomena biochemistry biomolecular nuclear magnetic resonance factual databases humans internet magnetic resonance spectroscopy mass spectrometry metabolic diseases metabolic networks and pathways metabolism metabolome organ transplantation quality control user-computer interface

I2D Database Content

http://ophid.utoronto.ca/ophidv2.201/ [open in a new window]

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Human Genome > Databases
Model Organisms > Databases
Protein > Networks & Interactions, Pathways and Enzymes

To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database.

links directory index: 300
TitlePublication YearGoogle Scholar Citation Count
Online predicted human interaction database2005300
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tagsconserved sequence database management systems fungal proteins gene expression profiling human genome humans information storage and retrieval internet molecular evolution online systems protein binding protein databases protein interaction mapping proteins proteome systems biology user-computer interface
setsUniversity of Toronto

KEGGDatabase Content

http://www.genome.ad.jp/kegg [open in a new window]

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Model Organisms > Databases

The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.

links directory index: 653
TitlePublication YearGoogle Scholar Citation Count
KEGG for integration and interpretation of large-scale molecular data sets201235
KEGG for representation and analysis of molecular networks involving diseases and drugs2010618
NAR Database Issue 2010
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tagsalgorithms animals biotransformation carbohydrate sequence chemical phenomena chemistry computational biology computer communication networks disease environment enzymes factual databases genes genetic databases genome genomics human genome human genome project humans information storage and retrieval internet japan knowledge bases ligands metabolism molecular biology molecular sequence annotation molecular sequence data nucleic acid databases pharmaceutical preparations pharmacological phenomena protein binding protein databases protein interaction mapping proteins signal transduction software systems biology systems integration tertiary protein structure user-computer interface

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html [open in a new window]

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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.

links directory index: 3841
TitlePublication YearGoogle Scholar Citation Count
MEME SUITE: tools for motif discovery and searching2009174
MEME: discovering and analyzing DNA and protein sequence motifs2006507
Meta-MEME: motif-based hidden Markov models of protein families1997223
An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases199757
The megaprior heuristic for discovering protein sequence patterns199628
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool199697
The value of prior knowledge in discovering motifs with MEME1995492
Fitting a mixture model by expectation maximization to discover motifs in biopolymers19942263
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 base sequence binding sites biopolymers computer communication networks databases as topic dna dna sequence analysis evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases internet mammals markov chains molecular models molecular sequence data nucleic acid repetitive sequences protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements user-computer interface

MetaboAnalyst 2.0Tool Content

http://www.metaboanalyst.ca [open in a new window]

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Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Proteomics

MetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various univariate and multivariate statistical analysis for two/multi-group, one/two-factor, as well time-series data. For targeted metabolomic data, users can also perform functional enrichment analysis and pathway analysis. New features for data filtering, editing & normalization

This content is being maintained by Jeff Xia.

links directory index: 75
TitlePublication YearGoogle Scholar Citation Count
MetaboAnalyst: a web server for metabolomic data analysis and interpretation200975
NAR Web Server Issue 2009NAR Web Server Issue 2012
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tagsbiomolecular nuclear magnetic resonance cluster analysis internet mass spectrometry metabolomics software user-computer interface

MIPSDatabase Content

http://www.helmholtz-muenchen.de/en/ibis [open in a new window]

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Model Organisms > General Resources
Model Organisms > Other Organisms
Model Organisms > Plants
Model Organisms > Yeast
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.

links directory index: 703
TitlePublication YearGoogle Scholar Citation Count
MIPS: curated databases and comprehensive secondary data resources in 201020119
MIPS: analysis and annotation of proteins from whole genomes2004422
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics200487
MOsDB: an integrated information resource for rice genomics200317
Sputnik: a database platform for comparative plant genomics200350
The PEDANT genome database2003118
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tagsanimals arabidopsis arabidopsis proteins biological models complementary dna computational biology data mining dna transposable elements expressed sequence tags fungi gene duplication genetic databases genome genomics humans information storage and retrieval internet metabolomics mice micrornas neoplasm genes nucleic acid databases nucleic acid sequence homology oryza sativa phenotype plant genes plant genome protein binding protein databases protein interaction mapping protein sequence analysis proteins proteomics saccharomyces cerevisiae proteins sequence homology software systems integration user-computer interface

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