User:R. Eric Collins/MBL/Rokas

From OpenWetWare
Jump to: navigation, search

Antonis Rokas

Evolutionary Genomics

  • Kahn 2011 increase in sequencing quality over time
  • CRAP: Cluster Reconstruction ... Phylogeny
    • find HGT of GAL cluster from Candida
    • Slot and Rokas 2010 PNAS
  • sarcosine oxidase
    • gene trees --> species trees
    • map environmental sequences to tree (iTOL) in a heatmap, colors = environment type/source
  • OASES seems to be the most popular for assembly
  • Di-Align (?) local alignment a la pplacer
  • Hittinger et al. 2010: using transcriptome to reconstruct species phylogenies
    • they needed 0.5--2 million 35bp reads from each species to get resolved phylogeny
    • reads assembled with velvet
    • contigs > 100bp, >300bp kept
    • identify RBBH "orthologs" __against outgroup__
    • keep loci with >1-4 species
    • locally align each cluster
    • concatenate
    • these will tend to be the most highly expressed regions
    • at $100/Gb this is coming to $10-50 per species