Daily Dozen:
1. List five things you could ascertain from an alignment between related proteins from two species.
2. What more could you determine by aligning the DNA sequence encoding the proteins?
3. Given a sequence alignment, how would you decide its significance?
4. What's the difference between Needleman-Wunsch and Smith-Waterman alignment?
5. What is dynamic programming?
6. What is the significance of off-diagonal matches in a dot matrix plot?
7. What does the word "indel" mean and why do we use it?
8. Exercise (this uses the NCBI BLAST tools): pick a protein. Try something well defined like p53 if you don't already have a protein in mind. Use BLAST to align it to the database. Pull out half a dozen of its matches and align them to the starting protein and to each other, pairwise, using blast2sequences. What differences do you see between database searches and pairwise alignments?
1. List five things you could ascertain from an alignment between related proteins from two species.
2. What more could you determine by aligning the DNA sequence encoding the proteins?
3. Given a sequence alignment, how would you decide its significance?
4. What's the difference between Needleman-Wunsch and Smith-Waterman alignment?
5. What is dynamic programming?
6. What is the significance of off-diagonal matches in a dot matrix plot?
7. What does the word "indel" mean and why do we use it?
8. Exercise (this uses the NCBI BLAST tools): pick a protein. Try something well defined like p53 if you don't already have a protein in mind. Use BLAST to align it to the database. Pull out half a dozen of its matches and align them to the starting protein and to each other, pairwise, using blast2sequences. What differences do you see between database searches and pairwise alignments?