Gene Finding Guide

Gene Finding 101: Working in Protein Space

  1. Obtain the sequence of a gene of interest, perhaps from A. thaliana
  2. Use the "tblastn" tool: This will reveal EXONS in the genomic data.
    1. The query is the protein sequence
    2. The Target is the set of BB scaffolds
    3. This tool translates the protein sequence into all 6 reading frames on the target.
  3. Examine the high scoring pairs (HSPs) for coverage.
  4. Consider additional extrinsic evidence from EST or mRNA alignments from tools like GMAP.
  5. Consider additional intrinsic evidence from Gene Prediction tools like Augustus.