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Assignment 8 Review Bio5488 3/31/2017
Adapted from Mayank
Don’t hesitate and ask questions early!
Longest ORFs? (1)
(2)
(3)
ORFs CONTIG#1
| ATG
| Stop
|
|
|
ATG
ATG
ATG
| Stop
| ATG
| Stop
• ORFs are mutually exclusive -> 2 ORFs in a certain frame cannot share the same start or stop codon • One possible strategy: start searching for a new start codon (ATG) only after the position you encountered the last stop codon (start codons between a start and a stop are ignored).
Is my call_orfs.py working? Online tools that do similar work? • http://www.ncbi.nlm.nih.gov/orffinder/ <- a useful tool for checking ORFs Notes for this tool: 1: an ORF is allowed to run to the end of the contig (no STOP codon required) 2: it only reports the longest ORF
More tools? • See http://en.wikipedia.org/wiki/Open_reading_frame
Take home messages: • Small changes in prediction model input
-> large changes in output • Gene prediction -> identify new potential genes from unknown
• Many methods exist for annotation -> performance comparison + check for assumptions • Non-ATG start codons exist in prokaryotic genomes! They still code for a modified Met (fMet)
