Fish Comparative Genomics: Difference between revisions

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*Table of fish genomes publicly available in CoGe
*<br>


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{| width="868" cellspacing="1" cellpadding="1" border="1" height="840"
|+ Table of fish genomes publicly available in CoGe
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| Species
| Common name
| Bioproject ID
| CoGe Genome Links
| Species notes
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*Links to CoGe [[Notebooks]] containing these genomes<br>  
*Links to CoGe [[Notebooks]] containing these genomes<br>  
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**[ GenomeList for all fish genomes in CoGe]
**[ GenomeList for all fish genomes in CoGe]


[https://genomevolution.org/r/egv4 All annotated unmasked fish genomes available in CoGe]
[https://genomevolution.org/r/egv4 All annotated unmasked fish genomes available in CoGe]  


[https://genomevolution.org/r/egv5 All unmasked fish genomes available in CoGe]
[https://genomevolution.org/r/egv5 All unmasked fish genomes available in CoGe]

Revision as of 18:17, 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
Species Common name Bioproject ID CoGe Genome Links Species notes



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=7145"