1. Gene Annotation with DNA Subway

2. or
Google ‘DNA Subway’

6. Google ‘ncbi’ or www.ncbi.nlm.nih.gov/

10. It is essential that the search for genes is done in regions that do not contain repetitive DNA.

11. It is essential that the search for genes is done in regions that do not contain repetitive DNA.

19. Gene predictors are inaccurate.
FGenesH and SNAP are ab initio scripts (use the algorithm only).
Augustus, is evidence-based, and tries to incorporate cDNA and EST data
Augustus and FGenesH are better at finding intron/exon boundaries while SNAP tends to report genes as single exons.

24. Time to integrate more evidence
Basic Local Alignment Search Tool or BLAST
BLASTn- uses the 102 kb DNA sequence as a query against all the A. thaliana sequences in GenBank.
BLASTx takes the 102 kb DNA and translates all six possible reading frames and uses all ORFs as a query against the GenBank proteins.

28. For students- Review Red Line with other clones.
Analyze 50 kb of sequence:

29. End of Exercise 1