Fish Comparative Genomics: Difference between revisions
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== Setting the hook: getting data loaded into CoGe == | == Setting the hook: getting data loaded into CoGe == | ||
*Loading new genomes into CoGe | *Loading new genomes into CoGe | ||
**Loading from the iPlant Data Store When loading a new genome | **Loading from the iPlant Data Store When loading a new genome | ||
**Using FTP/HTTP links for uploading genomes | **Using FTP/HTTP links for uploading genomes | ||
**Direct upload | **Direct upload | ||
**NCBI Loader <br> | **NCBI Loader <br> | ||
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*Table of fish genomes publicly available in CoGe | |||
{| width="1075" cellspacing="1" cellpadding="1" border="1" height="1387" |- | <b>Class</b> | <b>Order</b> | <b>Genus species </b> | <b>Common name</b> | <b>Notes</b> | <b>CoGe Genome Links</b> |- | Cephalaspidomorphi | Petromyzontiformes | Lethenteron camtschaticum | Artic lamprey | One of few extant jawless fish | |- | | | Petromyzon marinus | Sea lamprey | One of few extant jawless fish | |- | Chondrichthyes | Chimaeriformes | Callorhinchus milii | Australian ghostshark | Proposed model cartilaginous fish | |- | Sarcopterygii | Coelacanthiformes | Latimeria chalumnae | Coelacanth | Oldest known extant Sarcopterygii | |- | Actinopterygii | Anguilliformes | Anguilla japonica | Japanese eel | Ecological model, Industry species | |- | | Beloniformes | Oryzias latipes | Medaka | Model fish, Japanese pet fish | |- | | Characiformes | Astyanax mexicanus | Mexican tetra | Two forms: seeing, and cave-dwelling blind | |- | | Cichliformes | Haplochromis burtoni | Burton’s mouthbrooder | Ecological model species, Aquarium species | |- | | | Labeotropheus fuelleborni | Blue mbuna | | |- | | | Maylandia zebra | Zebra mbuna | Ecological model species, aquarium fish | |- | | | Mchenga conophoros | | | |- | | | Melanochromis auratus | Auratus cichlid | Phenotypic and ecological diversity | |- | | | Neolamprologus brichardi | Princess cichlid | Aquarium fish | |- | | | Oreochromis niloticus | Nile tilapia | Industrial species | |- | | | Pundamilia nyererei | | | |- | | Cypriniformes | Danio rerio | Zebrafish | Model species | |- | | | Pimephales promelas | Fathead minnow | Industrial baitfish | |- | | Cyprinodontiformes | Cyprinodon variegatus | Sheepshead minnow | Toxicology model | |- | | | Nothobranchius furzeri | Turquoise killifish | Short life span model species, metabolic diapause | |- | | | Nothobranchius kuhntae | Beira killifish | Short life model species | |- | | | Poecilia formosa | Amazon molly | Gynogenesis: all female populations | |- | | | Poecilia reticulata | guppy | Model species, aquarium fish | |- | | | Xiphophorus maculatus | Southern platyfish | Gives live birth | |- | | Esociformes | Esox lucius | Northern pike | Angling species | |- | | Gadiformes | Gadus morhua | Atlantic cod | Industrial species | |- | | Perciformes | Anoplopoma fimbria | Sablefish | Industrial species | |- | | | Dicentrarchus labrax | European seabass | Industrial species | |- | | | Gasterosteus aculeatus | Three-spined stickleback | Model species | |- | | | Sebastes nigrocinctus | Tiger rockfish | Angling species, long lived model, live bearer | |- | | | Sebastes rubrivinctus | Flag rockfish | Angling species, industrial species | |- | | | Stegastes partitus | Bicolor damselfish | Medical model species | |- | | Pleuronectiformes | Cynoglossus semilaevis | Tongue sole | Industrial species | |- | | Salmoniformes | Oncorhyncus mykiss | Rainbow trout | Angling species, Indrustrial species | |- | | Semionotiformes | Lepisosteus oculatus | Spotted gar | | |- | | Scombriformes | Thunnus orientalis | Pacific bluefin tuna | Industrial species | |- | | Tetraodontiformes | Takifugu flavidus | Sansaifugu | | |- | | | Tetraodon nigroviridis | Spotted green pufferfish | Model species, low amount of repetitive sequence | |- | | | Takifugu rubripes | ‘Fugu’ pufferfish | Shortest vertebrate genome | |} | |||
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*Links to CoGe [[Notebooks]] containing these genomes<br> | *Links to CoGe [[Notebooks]] containing these genomes<br> | ||
Revision as of 22:14, 5 December 2014
Summary/Abstract
Introduction
- Phylogeny of genomes with polyploidy events marked
Setting the hook: getting data loaded into CoGe
- Loading new genomes into CoGe
- Loading from the iPlant Data Store When loading a new genome
- Using FTP/HTTP links for uploading genomes
- Direct upload
- NCBI Loader
- Table of fish genomes publicly available in CoGe
- Links to CoGe Notebooks containing these genomes
- All unmasked fish genomes available in CoGe
- [ All masked fish genomes available in CoGe]
- All unmasked fish genomes available in CoGe
- Link to GenomeList for notebooks
- [ GenomeList for all fish genomes in CoGe]
Glossary
Analyses
Whole genome syntenic analysis
- SynMap
- Identify Whole Genome Duplications
- Identify Synteny
- Synonymous/nonsynonymous gene pair evolution
Microsyntenic analysis
- GEvo
- Validate microsynteny
- Identify Conserved non-coding sequences (regulatory function)
Ortholog/paralog finding with synteny
- SynFind
- Identify orthologous regions across many species
Gene family analysis
- CoGeBlast
- Identify many gene family members within/across species
- Extract sequences (nucleotide/protein)
- Phylogenetic tree reconstruction using iPlant/iAnimal for multiple sequence alignment and tree building
Functional genomics
- Adding/visualizing RNAseq data
Adding new data (genomes, RNASeq, SNPs) to CoGe
- LoadGenome
- LoadExperiment
- Keeping data private and sharing with collaborators
Discussion/Conclusions