Genome annotation for pea aphid, Acyrthosiphon pisum.
Search by Fields, and
see this Aphid Genes Search example
for help finding genes of interest.
This genome annotation was done with currently available, open source genome
annotation software. Analyses were run on TeraGrid,
as a test case for a GMOD Genome Grid
community genome analysis system.
These data are BLAST-able
and GBrowse-able .
The data are also at
-- Don Gilbert, June 2008
Name Last modified Size Description
Parent Directory 19-Jun-2008 13:51 -
aphid_dggsupl/ 24-Apr-2009 16:16 -
dupgenes/ 23-Sep-2008 20:53 -
fasta/ 16-Feb-2009 00:58 -
dgil_genomegrid_methods.txt 15-Aug-2008 13:21 2k
aphid-search-help.txt 31-Jul-2008 14:45 6k
bmc_pea_aphid_genome_release.txt 16-Jun-2008 00:28 7k
This directory has computed annotations for the first draft genome sequence release (Acyr_1.0)
of the pea aphid, Acyrthosiphon pisum.
These data have been produced at the Genome Informatics Lab, Indiana University,
by Don Gilbert, June 2008. Find out more at http://insects.eugenes.org/species/
16-jun-2008 NOTICE: there is a SCAFFOLD-ID mismatch between NCBI Gnomon gene models and
the genome assembly used here. This will be corrected shortly by
changing scaffold IDs to new ones. The gene models can be used, but scaffold IDs
in GFF location files will change soon.
Contents in brief:
- dgil_genomegrid_methods.txt -- methods and data used
- annotation/ -- computationally annotated gene predictions
- augustus/ -- results of Augustus gene finding
- evm/ -- results of EVidenceModeler combined gene models
- exonerate/ -- results of exonerate-mapped protein genes
- pasa_out/ -- results of PASA cDNA/EST assembly pipleline
- blast_db/ -- NCBI BLAST formatted genome assembly, cDNA/EST and
gene model proteins,
searchable at this BLAST service
- gbrowse_db/ -- GBrowse database (Lucene indices),
viewable at this Genome Map service
- fasta/ -- collected sequence data sets, with dna assembly, cDNA assembly,
and predicted proteins
- gff/ -- annotation locations on assembly (GFF v3 format)
- predict/ -- annotation prediction locations and fasta (duplicates of above)
- bmc_pea_aphid_genome_release.txt --
Genome data assembly description and data release policy from
Baylor College of Medicine