Download Exercise

Gene Annotation with DNA
Subway
• http://dnasubway.iplantcollaborative.org/
or
Google ‘DNA Subway’
Google ‘ncbi’ or www.ncbi.nlm.nih.gov/
It is essential that the search for genes is done in
regions that do not contain repetitive DNA.
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.
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.
For students• Review Red Line with other clones.
• Analyze 50 kb of sequence:
End of Exercise 1