24 April 2014


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Thursday notes


As a complement to topGO approach, use DAVID to focus on genes with high-quality annotations in model organisms Apis and Drosophila.

Get these BLAST hits using method for annotation I tried before going to FastAnnotator.

  • Found Taxids on NCBI for
  • Apis Taxid: 7459
  • Drosophila Taxid: 7215
  • Searched Entrez Protein Database with query txid7215[ORGN] OR txid7459[ORGN]
  • Selected “Send to File” wiht format “GI list”
    • generated list of 585,719 unique gi ids
  • Used list of GIs from the previous step with the blastdb_aliastool to build an aliased blastdb of just insects:

    blastdb_aliastool -gilist apis_drosophila.gi.txt -db nr -out nr_apis_drosophila -title “Apis and Drosophila nr database”

which gave output:

Converted 585719 GIs from apis_drosophila.gi.txt to binary format in nr_apis_drosophila.p.gil Created protein nr_apis_drosophila BLAST (alias) database with 274099 sequences (out of 585719 in nr_apis_drosophila.p.gil, 47% found)

  • Tested search against new (aliased) database:

    blastx -query query.fa -db nr_insecta -out querytest


Now…for the blastx of the whole caboodle, given problems I had before, trialed and used GNU parallel as described on Biostars to efficiently use all cores.

Test script for 50 sequences

cat ../test.fa | parallel --block 100k --recstart '>' --pipe blastx -evalue 0.01 -outfmt 6 -db /home/data/databases/ncbi_db/nr_apis_drosophila -query - > result

Moved analysis to Mason cluster - already had NCBI nr database downloaded there. Started script running…


Meet with Grace to go over results.

Ideas for continuation of Grace’s project:

  1. Positive control - use juvenile hormone which is known to promote foraging (Page et al. unknown)
  1. If this works (e.g. treated callows more likely to become foragers), test suite of other environmental factors:
  • paraquat
  • infection
  • development-heat stress
  • etc.
  1. Otherwise, initiate new experiment:
  • thermal adaptation of Aphaenogaster along elevational gradients in VT
  • gene expression response to fungal infection


  • Sara Helms Cahan, Christopher J. Graves, Colin S. Brent, (2011) Intergenerational Effect of Juvenile Hormone on Offspring in Pogonomyrmex Harvester Ants. Journal of Comparative Physiology B 181 991-999 10.1007/s00360-011-0587-x
  • Robert E. Page, Ricarda Scheiner, Joachim Erber, Gro V. Amdam, (unknown) Current Topics in Developmental Biology. Unknown

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