Fish Comparative Genomics: Difference between revisions
Jump to navigation
Jump to search
| Line 14: | Line 14: | ||
* [[Ortholog]] | * [[Ortholog]] | ||
* [[Paralog]] | * [[Paralog]] | ||
* [[Out- | * [[Out-Paralog]] | ||
* [[In- | * [[In-Paralog]] | ||
==Analyses== | ==Analyses== | ||
===Whole genome syntenic analysis=== | ===Whole genome syntenic analysis=== | ||
Revision as of 17:44, 21 November 2014
Summary/Abstract
Introduction
Data
- Phylogeny of genomes with polyploidy events marked
- Table of fish genomes used in this tutorial
- Links to CoGe Notebooks containing these genomes
- Link to GenomeList for notebooks
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