[Arthropod] New genome informatics for arthropod genomicists, talk slides

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Wed Dec 16 10:21:22 EST 2009



Dear folks,

Find here for those who may be interested an outline in slide format
of my current genome informatics methods as applied to various new
arthropod genomes.

  New genome informatics for insect [arthropod] genomicists 
  by Don Gilbert, Biology Dept., Indiana University
  talk at Entomological Society of America, 14 Dec 2009
  http://wfleabase.org/docs/all-docs/esangi0912-new-genome-informatics.pdf 

Overview
1. Current Genome Annotation Recipe 
2. ESTs give essential genome gene-set 
   .. but not all genes found by ESTs 
   .. EST and gene structure statistics of selected arthropod genomes
3. Next-gen base-level expression measures gene expression better 
   .. Tiling/RNA-seq Expression Recipe
   Tiling and RNA-seq find many new, weakly expressed genes 
4. RNA-Seq finds gene structures well 
   .. RNA-Seq Genes Recipe 
   .. the new EST? the new gene finder? Maybe
   
You can find here the answers (if not explicitly) to these questions
I posed a few weeks back:

> The species include arachnid tick Ixodes, the crustacean waterflea Daphnia, 
> and 4 insects: Bombyx silk moth, Drosophila fruitfly, Nasonia wasp 
> and Acyrthosiphon aphid.  You can find some extreme results among these:
> 
> - Which of these have official gene models that missed over 50% 
> of EST assemblies? 
> 
> - Which of these have 3 times more ESTs split between scaffolds, and
> a perhaps corresponding missed coding exon per gene model, on average?
>

- Don Gilbert
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd from indiana.edu--http://marmot.bio.indiana.edu/



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