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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