Genomics Demonstration

Goal: Find out what the Mystery Sequence is and to which metabolic pathway it belongs

Go to the JGI website. The Joint Genome Institute is responsible for a lot of sequencing of environmental microbes, especially those relating to energy, climate, geobiology, etc.
click on Find Genes --> BLAST
Enter the mystery sequence into the text box
Change the Program to 'blastx'. This will translate the DNA sequence into all 6 possible amino acid sequences and search for matches between them and a database of protein sequences from all available complete microbial genome sequences
Click 'Run Blast'
When the program has finished running, scroll down to the alignments showing the best matches.
How good is the hit? The Expect value (e-value) tells you about how probable it is that the hit is due to chance. For amino acid sequences, anything smaller than 1e-5 is considered a pretty good match. For nucleotide sequences, a more conservative 1e-10 may be used. For finding homologs (genes that share a common ancestor) or orthologs (genes that have diverged through speciation) it may be necessary to use more sophisticated methods of calling hits, because paralogs (genes that have duplicated within a genome) or convergent evolution can complicate matters, and matches to only a shared 'domain' (a 'self-contained' building block out of which proteins are formed) can lead to spurious hits.