Fish Comparative Genomics
Summary/Abstract
Introduction
Data
- Phylogeny of genomes with polyploidy events marked
- Table of fish genomes used in this tutorial
Class | Order |
Genus species |
Common name |
Notes |
Cephalaspidomorphi |
Petromyzontiformes |
Lethenteron camtschaticum |
Artic lamprey |
One of few extant jawless fish |
- 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