Why the “once a gap, always a gap” rule? Is it an insertion or a deletion? Does it matter? Why might there be a bacterial homolog? What about the gap? How would you handle the “gap penalty?”

Bioinformatics Homework

1.Why the “once a gap, always a gap” rule? Is it an insertion or a deletion? Does it matter?
2.Why might there be a bacterial homolog? What about the gap? How would you handle the “gap penalty?”
3.Find out what you can about Clustal Omega.
4.For those more familiar with HMMs, try to explain what the arrows mean. Feel free to refer to the original paper on ProbCons.