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Genome annotation for pea aphid, Acyrthosiphon pisum.

BLAST ... GBrowse map ... [?] Aphid gene annotations

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 ftp://eugenes.org/eugenes/genomes/aphid/

-- Don Gilbert, June 2008

      Name                             Last modified       Size  Description

[DIR] Parent Directory 19-Jun-2008 13:51 - [   ] annotation - [TXT] aphid-search-help.txt 31-Jul-2008 14:45 6k [DIR] aphid_dggsupl/ 24-Apr-2009 16:16 - [   ] augustus - [   ] blast_db - [TXT] bmc_pea_aphid_genome_release.txt 16-Jun-2008 00:28 7k [TXT] dgil_genomegrid_methods.txt 15-Aug-2008 13:21 2k [DIR] dupgenes/ 23-Sep-2008 20:53 - [   ] evm - [   ] exonerate - [DIR] fasta/ 16-Feb-2009 00:58 - [   ] gbrowse_db - [   ] gff - [   ] pasa_out - [   ] predict -

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

Developed at the Genome Informatics Lab of Indiana University Biology Department