[Arthropod] Daphnia pulex Genes 2010 (beta3)

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Sat Apr 24 14:55:39 EST 2010


Dear arthropod enthusiasts,

There is a new, improved gene prediction/evidence set for Daphnia
pulex, in a beta release, for those interested.  Your comments to
improve these are desired.

This is a much improved gene set. While there are many more
genes, most are supported by evidence.  Protein homology evidence
is extensive now, and suggests that Daphnia's gene set is one of
the most complete among arthropods, with more Human orthologs
than any other available arthropod genome.  

Notable stats for this Daphnia Genes2 set vs the 2007 official gene set 1:
  * Daphnia2 recovers 82% of protein homology, versus 42% for Daphnia1
  * Daphnia2 recovers 90% of ESTs, versus 75% for Daphnia1
  * Daphnia2 recovers 66% (5Mb) of genome tile expression not in Daphnia1

Daphnia has best matches and longest alignments to human and
other model eukaryote gene sets (Tribolium has the best of the
insects).  This update improves on this.
  Best matches to Human genes among 14 arthropod genomes:
     Daphnia2 has 44% of these, vs 21% for Daphnia1.
     Ixodes has 15%, Tribolium has 10%, and a slim 2% for Drosophila mel.
  Alignment to Human genes: Daphnia2 averages 191 aminos, 188 aa for Daphnia1
     187 aa for Tribolium, and 175 aa for Drosophila.
  Percent of 20,000 Human genes found: 71% for Daphnia2, 69% for Daphnia1, 
     68% for Tribolium, 66% for DrosMel

There are problems yet in this gene set that I will fix; a final
version may be out in a few months.

Find these annotated genes in GFF and protein fasta formats here
  http://server7.wfleabase.org/prerelease4/gene-predictions/

Also see this poster from the recent Daphnia Genomics meeting
with comments on these new gene predictions.
  http://wfleabase.org/docs/all-docs/daphnia-genomes-crossroads10.pdf

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



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