Daphnia pulex Genes 2010

This 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.
-- Don Gilbert, gilbertd at indiana edu.

Genome map view of genes
Daphnia genomes at the crossroads, 2010 poster with comments on new genes.
Sample gene map views, including Hemoglobin cluster, Rhodopsin, Chorion peroxidase and beta-galactosidase gene clusters

 Name                                           Last modified       Size  Description

 Parent Directory                               08-Jan-2015 13:14      -  
 daphnia_genes2010_pix/                         24-Apr-2010 15:08      -  
 daphnia_genes2010_tilex/                       01-Dec-2010 09:34      -  
 older-predictions/                             22-Apr-2010 18:25      -  
 daphnia_genes2010_header.html                  24-Apr-2010 14:42     1k  
 dpx-augustus-predict0802.txt                   17-Dec-2008 23:39     4k  
 daphnia_genes2010_beta3.readme.txt             28-Jan-2011 13:14    10k  
 daphnia_genes2010_cuticle.txt                  08-Jul-2010 18:38    17k  
 daphnia_genes2010_human_unique.txt             06-Jul-2010 22:07    27k  
 daphnia_genes2010_cuticle.chitbindrr1genes.txt 08-Jul-2010 19:01    49k  
 daphnia_genes2010_beta3_alttr.gff.gz           22-Apr-2010 21:35   130k  
 daphnia_genes2010_exonutr.gff.gz               03-Dec-2010 16:44   1.4M  
 daphnia_genes2010_beta3.annotation.txt.gz      23-Dec-2010 13:01   2.3M  
 daphnia_genes2010_exonutr5prime.fa.gz          19-Mar-2014 19:55   3.2M  
 daphnia_genes2010_beta3.gff.gz                 23-Apr-2010 22:24   8.0M  
 daphnia_genes2010_exonutr3prime.fa.gz          19-Mar-2014 19:56   8.4M  
 daphnia_genes2010_beta3.aa.gz                  22-Apr-2010 20:43   9.1M  
 daphnia_genes2010_beta3.cds.gz                 28-Jan-2011 12:44  15.3M  
 daphnia_genes2010_beta3.tr.gz                  27-Jan-2011 12:36  22.7M


daphnia_genes2010_beta3  : Daphnia pulex Gene Set 2.0 beta3, 2010 April
   see daphnia_genes2010_beta3.readme.txt

daphnia_genes2010_tilex/  : Tile expression analysis for Genes 2.0

older-predictions/
dpulex_aug26_mix14_beta2 : Daphnia pulex Gene Set 2.0 beta2, 2010 March

dpulex_augustus19.gff,aa : protein coding gene predictions/calls derived
from Augustus+ for Daphnia pulex using (a) model trained on Daphnia pulex
EST/cDNA (PASA), (b) Transcriptionally active regions (TARs) from genome tile
array.  TAR data guided individual predictions.  Some will be outside tar regions,
some matching. The mRNA attribute pct_evd= provides percentage of gene supported
by TAR data.

dpulex-augmap19-nojgigene.esum  : for augmap genes outside of prior predictions,
	homology check with blast NCBI-Nr protein matches
dpulex-tar-all.gff.gz           : TAR combined data (3 groups: fem,male,metal, 3 levels)
dpulex_augustus19.aa.gz         : predicted proteins
dpulex_augustus19.gff.gz        : predicted features

Don Gilbert, 2008 .. 2010