30 May 2014

BLAST, RefSeq, DAVID, aster, and species distribution models

Next post Previous post

May 26 - 30 notes



For working with DAVID database, needed gene IDs for high quality reference hits. Used the RefSeq protein database targeting Apis mellifera and Drosophila as preliminary examination by Sara showed these returned the most hits that were in the DAVID database.

The following script

  • downloads the RefSeq protein database,
  • makes a database alias for Apis mellifera and Drosophila as explained here but using taxid 7460 for Apis mellifera. note that the ‘gi.list’ file needs to be created and in the directory before running the script
  • runs blastx in parallel creating a file in BLAST archive format


## download newest version of database using `update_blastdb.pl` script
update_blastdb.pl refseq_protein

## uncompress files
for filename in *.tar.gz
    tar zxf $filename

## make alias to A. mellifera and Drosophila
blastdb_aliastool -gilist ../amellifera_drosophila_gi.list -db refseq_protein -out refseq_protein_amellifera_drosophila -title "Apis mellifera and Drosophila Refseq Protein database"

# blastx using GNU parallel 
cat $transcriptome | parallel -j 8 --block 100k --recstart '>' --pipe blastx -evalue 0.01 -max_target_seqs 1 -outfmt 11 -db  refseq_protein_amellifera_drosophila -query - > ApTranscriptome_parallel_blastx_refseq_protein_amellifera_drosophila

I then created a table format file with 1 hit per query using blast_formatter:

blast_formatter -archive ApTranscriptome_parallel_blastx_refseq_protein_amellifera_drosophila -max_target_seqs 1 -outfmt 6 -out test6

Of the initial 105k transcripts, 29,080 had BLAST hits to the Apis mellifera & Drosophila RefSeq protein database. This is the file I then used for DAVID.



Figuring out how to use rDAVIDWebService…


Centennial paper


Jay et al. 2012 Molecular Ecology

  • applying SDMs to genetic clusters prone to two errors
  • statistical errors in assignment of individuals to clusters would not be accounted for
  • inaccurate modeling of admixture
  • ancestry distribution models account for these two problems
  • project ancestry coefficients on geographic maps
  • limit the number of clusters to < 4 …. why?

Sork et al. 2010 Molecular Ecology

  • range-wide characterization of genetic structure of California valley oak
  • patterns of population relatedness using PopGraph
  • significant connectivity among populations, especially in north. evidence for long-distance gene flow along foothills. central valley a barrier for direct east - west gene transfer in south
  • correlations between nuclear genetic variation and climate variation
  • strong association
  • region-specific bioclimatic models (SDMs)
  • size and proximity of predicted suitable habitat varies considerably among regions, from nearly complete overlap to separation of > 100 km

D’Amen et al. 2013 Global Ecology and Biogeography

  • examination of how species-level niche modeling can bias evaluation of conservation requirements in presence of intra-specific variation
  • 10 mammal species in Africa with multi-gene phylogenetic trees
  • 3 sets of ecological niche models (ENMs)
  • ENM-S: standard species-level ENM
  • ENM-L: for each lineage within a species
  • ENM-C: composite to summarize across each lineage
  • species-level models substantially over-predict range expansion

Espindola et al. 2012 Ecology Letters

  • investigate distribution dynamics of cold-adapted globeflower
  • characterized population structure using STRUCTURE
  • niche-based SDMs to predict future species and population distribution
  • compared hind-casted SDMs to phylogeographic
  • simulated

Pease et al. 2009

  • identify lineages of California mule deer using Structure
  • significant overlap of lineages at LGM
  • present-day genetic divergence appears to be recent, driven by ecological factors


  • Meet with NG to discuss Centennial paper
  • Writing.
  • Working on DAVID analysis.
  • Meet with Scott Tighe at sequencing facility.
  • Went over protocol for bead purification and size selection using E-gels
  • very light DNA smear of post-PCR product. suggested we check PCR and do a titration with different # of cycles to confirm PCR is working

Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.