Fish Comparative Genomics

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Revision as of 18:11, 4 December 2014 by BJoyce (talk | contribs) (Data)
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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




































































































































































































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

Discussion/Conclusions