OH tomorrow

[Michael Brudno]

Hi Everyone,

The office hours tomorrow will be 10-11:45. I have someone else coming
in for an 11:45 meeting, so I'll have to finsh 15 minutes earlier than
originally planned.

Sorry,

-M

[Lev Naiman]

Some further questions:

1) 

a. Do matches and local alignment means the same in this context?

2)

a. Which should be the big O of the algorithm?

   How would we consider gaps in this exercise?

--
The statement below is true.
The statement above is false.

[Michael Brudno]

On Thu, Nov 18, 2010 at 10:51 PM, Lev Naiman <naim...@gmail.com> wrote:
> Some further questions:
> 1)
> a. Do matches and local alignment means the same in this context?

Yes

> 2)
> a. Which should be the big O of the algorithm?

It should be linear in the tree size for any fixed alphabet.

>    How would we consider gaps in this exercise?

Feel free to ignore them.

-M

[Recep Çolak]

On Fri, Nov 19, 2010 at 6:57 AM, Michael Brudno <bru...@gmail.com> wrote:

On Thu, Nov 18, 2010 at 10:51 PM, Lev Naiman <naim...@gmail.com> wrote:
> Some further questions:
> 1)
> a. Do matches and local alignment means the same in this context?

The reduction we covered in the class (and the one discussed in the handout) was based on character matches and this is how I extended the algorithm
 for the weighted case. However, if a match the same thing as local alignment, then that means there will be overlaps which is does not happen in the character based case.
Is it acceptable we solve the problem for chaining of character matches only or do we need to extend the LIS to rectangle/square shaped
local alignment chaining first and then to HSCS?

 

[Michael Brudno]

The intent was to extend *both* to the weighted case and to the fact
that you are chaining rectangles.

-Mike

2010/11/19 Recep Çolak <rco...@cs.toronto.edu>: