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General Resources

The resources listed here include tools and databases for general information on a variety of model organisms.

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Found 32 links

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JCatTool Content

http://www.jcat.de/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
JCat: a novel tool to adapt codon usage of a target gene to its potential expression host200581
NAR Web Server Issue 2005
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tagsalgorithms animals caenorhabditis elegans codon escherichia coli gene expression pseudomonas aeruginosa recombinant proteins species specificity

mGene.webTool Content

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

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DNA > Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources

mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
mGene: accurate SVM-based gene finding with an application to nematode genomes200927
mGene.web: a web service for accurate computational gene finding20098
NAR Web Server Issue 2009
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tagsalgorithms animals artificial intelligence caenorhabditis caenorhabditis elegans computational biology dna sequence analysis genes genomics helminth genes helminth genome proteins reproducibility of results reverse transcriptase polymerase chain reaction rna splice sites transcription initiation site

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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external linksLink on Wikipedia
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

NCBI Assembly ArchiveTool Content

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

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Model Organisms > General Resources

The NCBI Assembly Archive links publically available assembly information with the NCBI Trace Archive\'s raw sequence data.

links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
The genome Assembly Archive: a new public resource200420
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setsNational Center for Biotechnology Information (NCBI)

NCBI Taxonomy DatabaseDatabase Content

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

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DNA > Phylogeny Reconstruction
Model Organisms > General Resources
Protein > Phylogeny Reconstruction

Taxonomic classification of all organisms with sequences in GenBank.

links directory index: 1427
TitlePublication YearGoogle Scholar Citation Count
The NCBI Taxonomy database20124
Database resources of the National Center for Biotechnology Information2000464
GenBank2000959
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external linksLink on Twitter

NEWTDatabase Content

http://www.ebi.ac.uk/newt/display [open in a new window]

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DNA > Phylogeny Reconstruction
Model Organisms > General Resources
Protein > Phylogeny Reconstruction

NEWT is the taxonomy database maintained by the UniProt group.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
NEWT, a new taxonomy portal200339
NAR Web Server Issue 2003
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tagsclassification protein databases systems integration

OligoArrayTool Content

http://berry.engin.umich.edu/oligoarray2_1/ [open in a new window]

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Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > General Resources

OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequenced genome can be found at http://berry.engin.umich.edu/oligoarraydb/index.html

links directory index: 236
TitlePublication YearGoogle Scholar Citation Count
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach2003236
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tagsalgorithms arabidopsis gc rich sequence gene expression profiling genetic transcription nucleic acid conformation oligonucleotide array sequence analysis oligonucleotide probes plant genome thermodynamics

Ontology Lookup ServiceTool Content

http://www.ebi.ac.uk/ols [open in a new window]

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DNA > Annotations
DNA > DNA and Genomic Analysis
Model Organisms > General Resources

The Ontology Lookup Service provides interactive and programmatic interfaces to query and browse a suite of biomedical ontologies and controlled vocabularies. Users can also navigate the relationships between terms and obtain additional metadata and annotations. Improvements in 2010 have made OLS easier to use, capture more annotations from source data and integrate into external applications.

This content is being maintained by rglcote.

links directory index: 160
TitlePublication YearGoogle Scholar Citation Count
The Ontology Lookup Service: bigger and better20109
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries200849
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries2006102
NAR Web Server Issue 2008NAR Web Server Issue 2010
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tagscontrolled vocabulary database management systems factual databases natural language processing programming languages proteomics systems integration

PhenomicDBDatabase Content

http://www.phenomicdb.de/ [open in a new window]

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Model Organisms > General Resources
Protein > Annotation and Function
Sequence Comparison > Comparative Genomics

PhenomicDB integrates the genotype and phenotype information of several organisms from public data sources. The mapping of phenotypic data fields allows cross-species phenotype comparison.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics200541
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external linksLink on Wikipedia
tagsanimals documentation gene expression profiling genetic databases genomics genotype humans information dissemination phenotype species specificity

PhenomicDBDatabase Content

http://www.phenomicdb.de [open in a new window]

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Model Organisms > Databases
Model Organisms > General Resources

PhenomicDB a free multi-organism phenotype-genotype database unifying a variety of primary sources to make phenotypic data from a wide range of species and model organisms simultaneously searchable, visible and comparable. Gene orthology and similarity information mapped to particular entries, and the phenotypic data clustering system, provide facilities for the discovery of new phenotypic manifestations of a given genotype. Reported relationships are supported by evidence and reference links.

This content is being maintained by Ivanka_Karageorgieva_metalife.

links directory index: 74
TitlePublication YearGoogle Scholar Citation Count
Phenoclustering: online mining of cross-species phenotypes20104
PhenomicDB: a new cross-species genotype/phenotype resource200729
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics200541
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tagsanimals cluster analysis data mining documentation gene expression profiling genetic databases genomics genotype humans information dissemination phenotype rna interference species specificity

PhyloPatTool Content

http://www.cmbi.ru.nl/phylopat [open in a new window]

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Model Organisms > General Resources

PhyloPat is a webserver which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. The output can be saved in HTML, Excel or plain text format for further analysis. Output is linked to the FatiGO web interface creating easy access to functional information.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
PhyloPat: phylogenetic pattern analysis of eukaryotic genes200616
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tagsalgorithms automated pattern recognition base sequence chromosome mapping conserved sequence database management systems dna sequence analysis eukaryotic cells genetic databases molecular sequence data nucleic acid sequence homology phylogeny sequence alignment

PhytozomeDatabase Content

http://www.phytozome.net/ [open in a new window]

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Model Organisms > General Resources
Model Organisms > Plants
Sequence Comparison > Comparative Genomics

Comparative hub for plant genome and gene family data and analysis.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
Phytozome: a comparative platform for green plant genomics201213
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Pre EnsemblResource Content

http://pre.ensembl.org/index.html [open in a new window]

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

The Ensembl pre-build site provides displays of genomes that are in the process of being annotated.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
Ensembl 2012.201298
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setsEuropean Bioinformatics Institute (EBI)

The Sequence Ontology ProjectResource Content

http://www.sequenceontology.org/about/contacts.html [open in a new window]

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Human Genome > Other Resources
Model Organisms > General Resources

The Sequence Ontology Project aims to provide a standard vocabulary for describing biological sequences.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
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THREaD Mapper StudioTool Content

http://cbr.jic.ac.uk/threadmapper [open in a new window]

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DNA > Structure and Sequence Feature Detection
Human Genome > Genomics
Model Organisms > General Resources

THREaD Mapper Studio is a web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers.

This content is being maintained by Jo_Dicks.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps20102
NAR Web Server Issue 2010
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