Fish Comparative Genomics: Difference between revisions

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{| width="1016" cellspacing="1" cellpadding="1" border="1" height="827"
{| width="1016" cellspacing="1" cellpadding="1" border="1"
|+ Table of fish genomes publicly available in CoGe  
|+ Table of fish genomes publicly available in CoGe  
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| Class
| Species  
| Species  
| Common name  
| Common name  
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| CoGe Genome Links
| CoGe Genome Links
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| ''Lethenteron camtschaticum''
| Hyperoartia
| ''Lethenteron camtschaticum''  
| Artic lamprey  
| Artic lamprey  
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Revision as of 18:39, 8 January 2015

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
Class Species Common name Bioproject ID Species notes CoGe Genome Links
Hyperoartia Lethenteron camtschaticum Artic lamprey One of few extant jawless fish



All annotated unmasked fish genomes available in CoGe

All unmasked fish genomes available 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

Discussion/Conclusions


Retrieved from "https://genomevolution.org/wiki/index.php?title=Fish_Comparative_Genomics&oldid=7149"