Gene Finding 101: Working in Protein Space
- Obtain the sequence of a gene of interest, perhaps from A. thaliana
Use the "tblastn" tool: This will reveal EXONS in the genomic data.
- The query is the protein sequence
- The Target is the set of BB scaffolds
- This tool translates the protein sequence into all 6 reading frames on the target.
- Examine the high scoring pairs (HSPs) for coverage.
- Consider additional extrinsic evidence from EST or mRNA alignments from tools like GMAP.
- Consider additional intrinsic evidence from Gene Prediction tools like Augustus.