Fish Comparative Genomics: Difference between revisions
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*Links to CoGe [[Notebooks]] containing these genomes<br> | *Links to CoGe [[Notebooks]] containing these genomes<br> | ||
**[https://genomevolution.org/CoGe/NotebookView.pl?nid=890 | **[https://genomevolution.org/CoGe/NotebookView.pl?nid=890 All fish genomes available in CoGe]<br> | ||
*Link to [[GenomeList]] for notebooks | *Link to [[GenomeList]] for notebooks | ||
**https://genomevolution.org/r/ec6b | **https://genomevolution.org/r/ec6b | ||
Revision as of 21:42, 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