Genome Biology DNA60 Bioinformatics Challenge
If you are reading this page, then you must have successfully completed Step 1. Congratulations! For the second step, below, we have made things a little trickier...
Step 2: Gene finding
Step live from: Monday April 22nd 5 pm Eagle Time (6 pm CET/5 pm BST/noon ET/9 am PT)
Genome annotation can be a devilish task but nature was kind enough to invent an open reading frame-based genetic code, with distinct codons for STOP making the task of gene finding somewhat easier than it might have been. In fact, it was the very lack of an open reading frame that led to important discoveries about gene silencing and other ncRNA functions.
As with motif detection, gene finding is one of the older forms of bioinformatics. But in this challenge, we’ve added a bit of a twist…
For the Step 2 challenge, you will need to identify a secret phrase encrypted in a short genome. To unlock the code, you will need to do the following:
1) Identify all open reading frames (on both strands) in the genome from start codon (ATG) to stop codon (TAA, TAG, TGA)
2) Sort these open reading frames from longest to shortest
3) Translate the sorted open reading frames to their respective amino acid sequences
4) Select the 25th amino acid from the top 15 longest sequences to spell out the secret phrase
Once you have identified the secret phrase, you can use it to form the URL for Step 3.
For example, if the secret phrase were to be 'ELEMENTARYMYDEARWATSON', then Step 3's URL would be: http://genomebiology.com/about/update/DNA60_ ELEMENTARYMYDEARWATSON