JGI JAZZ assembly 2006-09-05 (8/9X) and annotations for Daphnia pulex: http://wfleabase.org/prerelease/dpulex_jgi060905/

est/ EST data set (JGI 2005/2006) :

daphnia-EST-group-table2.txt -- table identifying EST treatment groups
daphnia-EST-jgi20050825.fa.gz -- EST sequence (mostly Non-normalized libraries of table)
daphnia-EST-jgi20061205.fa.gz -- EST sequence (mostly Normalized libraries)
daphnia-EST-jgi200*.idllist -- linking tables of wFleabase, JGI ids

gff/ Annotations:

GFF - Gene finding format
Assembly scaffolds, EST locations, Genetic markers
PASA EST-assembly and gene model updates
Eukaryote model organism genes mapped to Daphnia genome
Gene prediction locations

genome-assembly/ Primary genome assembly data :

dpulex_jgi060905.fa.gz -- JGI JAZZ main scaffolds fasta
" .count -- faCount, table of base counts/scaffold
" .gapcount -- histogram of gap sizes in assembly

genome-assembly-full-jazz_20060901/ : Full JGI JAZZ assembler output file set

gene-predictions/ Gene Predictions:

dpulex_jgi060905_DGIL_SNO.gff.gz -- SNAP gene predictions, hmm bootstrapped on Dpulex genome
" .aa.gz -- amino predictions
" .tr.gz -- transcript predictions fasta

genetic-map/ Genome - Genetic Map correspondence:

dpulex-mapid_marker2.txt -- table of marker genetic map locations
dpulex-mapid_marker2s.fa -- marker fasta
dpulex_jgi060905-mapid.megablast -- marker blast to scaffolds.fa
dpulex-scaffold-map1.txt -- scaffold x genetic map from megablast results
dpulex-scaffold-map2.txt -- " (sorted by scaffold)

pasa/ PASA EST assembly analysis results : see PASA_gene_annotation

2008 Dec 09
Find here these various genome features
  http://wfleabase.org/release1/current_release/

This has the official gene predictions with exons,
  gff/dpulex-genepredict-v11.gff.gz  
  and is same as gene-predictions/dpulex_jgi060905_JGI_V11.gff.gz

These introns are computed from the above dpulex_jgi060905_JGI_V11 exons:
  supplement/introns/
    dpulex1_introns.JGI.gff.gz
    and dpulex1_intergene.JGI.gff.gz  for intergenic regions

tRNA genes are listed here 
   trna-ncrna/dpulex-tRNA_analysis2.gff
  
Repeats:
 repeats/dpulex-repeatmasker.gff2  : repeatmasker results from JH Choi
 repeats/dpulex_jgi060905-pilerpred.gff.gz:   770 repeats identified by PILER-DF by Chris Smith
 repeats/daphnia_ltr_table.gff  :  322 LTR transposons from Mike Lynch's colleague

gff/dpulex-polymorphisms_04_2007.gff.gz
 : SNP's from Abe Tucker, UNH
 
gff/dpulex-microsatellite.gff.gz   
 : has identified microsatellites

Here is a full list of ESTs mapped to the genome:
  pasa/pasa_daphc.validated_transcripts.gff3.gz