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Other Organisms

This section includes links to genome databases, resource centers, and consortiums for various other model organisms.

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Found 20 links

Displaying 15 links

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

Daphnia Genomics ConsortiumResource Content

http://daphnia.cgb.indiana.edu/

Model Organisms > Other Organisms

The Daphnia Genomics Consortium (DGC) is an international network of investigators committed to mounting the freshwater crustacean Daphnia as a model system for evolutionary / ecological genetics and genomics.

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DOE Joint Genome Institute Genome PortalDatabase Content

http://genome.jgi-psf.org/

Model Organisms > Fish
Model Organisms > General Resources
Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Plants

The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.

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E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

FluGenomeTool Content

http://www.flugenome.org/

Human Genome > Health and Disease
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching

FluGenome is a tool for determining lineages and genotypes of influenza A viruses.

NAR Web Server Issue 2007
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tagscomputational biology genetic databases genetic polymorphism genomics genotype influenza a virus orthomyxoviridae phylogeny viral genes viral genome viral proteins

Geno2phenoTool Content

http://www.geno2pheno.org/cgi-bin/geno2pheno.pl

Model Organisms > Other Organisms

Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.

NAR Web Server Issue 2003
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tagsalgorithms anti-hiv agents artificial intelligence automated pattern recognition cluster analysis computational biology computer-assisted drug therapy computing methodologies decision trees disease susceptibility dna sequence analysis drug combinations factual databases gene expression profiling genetic models genetic polymorphism genetic variation genotype hiv hiv infections hiv-1 humans innate immunity molecular sequence data phenotype pol genes regression analysis reproducibility of results sensitivity and specificity statistical models viral dna viral drug resistance viral genome

Genotyping - NCBITool Content

http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi

Model Organisms > Other Organisms
Sequence Comparison > Other Alignment Tools

The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.

NAR Web Server Issue 2004
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tagsalgorithms dna sequence analysis genetic recombination genotype hepacivirus hepatitis b virus hiv-1 molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

Influenza Virus ResourcesResource Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html

Model Organisms > Other Organisms

Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses.

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tagsanimals genetic recombination genetic variation genome h3n2 subtype influenza a virus human influenza humans influenza a virus influenza vaccines influenza virus hemagglutinin glycoproteins molecular evolution mutagenesis mutation neuraminidase new york phylogeny public sector reassortant viruses sequence analysis time factors viral genes viral genome virus replication

jpHMMTool Content

http://jphmm.gobics.de/

Model Organisms > Microbes
Model Organisms > Other Organisms

Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.

This content is being maintained by akschultz.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalgorithms amino acid sequence homology base sequence dna breaks genetic recombination genomics hiv-1 markov chains phylogeny proteins reproducibility of results sequence alignment tertiary protein structure viral genome

MIPSDatabase Content

http://mips.gsf.de/

Model Organisms > General Resources
Model Organisms > Other Organisms
Model Organisms > Plants
Model Organisms > Yeast
Protein > Interactions, Pathways, 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.

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tagsanimals arabidopsis arabidopsis proteins biological models complementary dna computational biology dna transposable elements expressed sequence tags fungi gene duplication genetic databases genome genomics humans mice nucleic acid databases nucleic acid sequence homology oryza sativa plant genes plant genome protein binding protein databases protein interaction mapping protein sequence analysis proteins proteomics saccharomyces cerevisiae proteins sequence homology

NCBI Influenza Virus Sequence Annotation ToolTool Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi

DNA > Annotations
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms

The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence dna sequence analysis genotype influenza a virus influenza b virus molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

Parasite-GenomeDatabase Content

http://www.ebi.ac.uk/parasites/parasite-genome.html

Model Organisms > Other Organisms

Parasite genome databases and genome research resources.

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PartiGeneDBDatabase Content

http://www.partigenedb.org/

Model Organisms > Other Organisms
Sequence Comparison > Comparative Genomics

PartiGeneDB is a database of about 300 partial genomes from eukaryotic organisms that have been assembled from EST data.

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tagsexpressed sequence tags genomics nucleic acid databases

Poxvirus Bioinformatics Resource CenterTool Content

http://www.poxvirus.org/

Model Organisms > Other Organisms

Includes poxvirus genomic sequences; annotation and analysis of poxvirus genes; web-based data mining and sequence analysis tools; software for analysis of complete genomes; literature resource; repository of poxvirus species and strains; discussion forum.

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Tags associated with subcategory 'Model Organisms/Other Organisms'

humans genomics viral genome computational biology animals sequence alignment algorithms genome base sequence genetic databases molecular sequence data viral genes dna sequence analysis database management systems phylogeny reproducibility of results proteins viral dna genotype factual databases genetic variation protein databases nucleic acid databases genetic polymorphism influenza a virus systems integration genetic recombination bacterial genome amino acid sequence homology amino acid sequence mice hiv-1 expressed sequence tags hiv infections pol genes regression analysis technology transfer protein sequence analysis statistical data interpretation hiv reference standards thermoplasma innate immunity genetic models cluster analysis computing methodologies computer-assisted drug therapy automated pattern recognition sensitivity and specificity viral proteins decision trees vaccinia virus gene expression profiling drug combinations disease susceptibility variola virus dna-binding proteins statistical models transcription factors hepacivirus small interfering rna sequence homology proto-oncogene proteins rna interference rna sequence analysis hepatitis b virus National Center for Biotechnology Information (NCBI) human genome project nucleic acid sequence homology genes dna viruses california human genome proteome phenotype cultured cells dna primers core binding factor alpha 2 subunit yeasts viral drug resistance fungi microbiological techniques double-stranded rna drosophila melanogaster inhibitor of apoptosis proteins insect genes indicators and reagents genomic library drosophila proteins essential genes gene knockdown techniques nucleotides programming languages chemical dictionaries gene expression initiator codon bacterial genes archaeal genome transcriptional regulatory elements anti-infective agents