Lesson 2_5: Strategy for Searching Gene Data Bases
Steve Graves is going to present a strategy (written 10/96) for taking a peptide sequence to a cloned DNA fragment for expression using the currently available databases. (Note that the reason he got X's in his output embedded in his query sequence is that he had filtering ON by default. The X'd regions have been removed. Filtering removes low complexity sequences from the search to avoid meaningless similarities. Check out the help links at NCBI to learn more.)
Assignment 2_5
Conduct a search of your own, using this dna sequence. Write an HTML document that describes what you found, including a physical map for the sequence. You might want to use your translation program to help you locate the reading frames that are relevant. Also, just for fun, try running the sequence through the program SEQSCAN. See any promoter and protein binding elements? (All in all, I find four interesting things about this sequence - do you?)
You may also want to check out a project done by Charles Ducker last year, in which he tried to identify protein binding sites in some DNA sequence of yeast. He came up with some interesting tools, and his project is well documented.