allignment matrix

[phillie]

Can someone explain to me how they filled in the matrix on this webpage:

http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast-29096

(figure 1-D or 1-F)

And more specific: I am talking about (for example)
the value -0 given at L(-4) and E(-2).

Because if I look at it and use their method of approach, it (I think) should not be -0 but -2 since the value on the left is -1 and its a mismatch, this making it -1 + - 1 giving -2 .. but they write a -0

And there are some other numbers in that matrix that I dont get, but this is just an example.

[muthu545]

Hi,

I looked at the matrix, the value of -0 for L and E comparison is right.
As per their explanation, you have to perform 3 computations.
First computation is [Upper] P ---> E = -3 + -1 (for mismatch) = -4
Second computation is [Left] L--->E = -4 + -1 (for mismatch) = -5
Third computation is [Upper-Left] E ---> E = -1 + 1 (for match) = 0

The max value in these 3 computations is 0. and it is reported for L and E

note: The values computed cannot exceed zero.

I hope this is helpful.

Thanks
--
Muthu

[phillie]

I am not sure how you did this:
As per their explanation, you have to perform 3 computations.
First computation is [Upper] P ---> E = -3 + -1 (for mismatch) = -4
Second computation is [Left] L--->E = -4 + -1 (for mismatch) = -5
Third computation is [Upper-Left] E ---> E = -1 + 1 (for match) = 0

+ if this is right, the arrow in that square should point to the upper left and not left since you used the upper left as the highest value.. (you used upper left to calculte 0)


upper (how I understand it) = the "green" square (see the previous figure where they colored he 3 squares you use to ciopmpute it, the upper score, above "0") this is -4 and since there is a mismatch, it becomes -4-1=-5

left for me is: -1 (the square on the left holds a value of -1) -1 for the mismatch = -2
Upper-left is: -3 + -1 for the mismatch= -4

I guess I am understanding it wrong, but I do not see how you do it using their explenation...



Where do you get the -3 and -4 for the upper and left?

[muthu545]

Hi
Sorry I had my labelings for upper, left and upper-left interchanged and confused you
First computation is [Upper-left] P ---> E = -3 + -1 (for mismatch) = -4
Second computation is [Upper] L--->P = -4 + -1 (for mismatch) = -5
Third computation is [Left] E ---> E = -1 + 1 (for match) = 0

And that is why you see a left arrow on he square...
I will edit this explanation in few mins... To make it more clear for yo
Thanks
--
Muthu

[phillie]

Hi
Sorry I had my labelings for upper, left and upper-left interchanged and confused you
First computation is [Upper-left] P ---> E = -3 + -1 (for mismatch) = -4
Second computation is [Upper] L--->E = -4 + -1 (for mismatch) = -5
Third computation is [Left] E ---> E = -1 + 1 (for match) = 0

And that is why you see a left arrow on he square...
I will edit this explanation in few mins... To make it more clear for yo
Thanks
--
Muthu

THis I can understand (at least the first 2).
(at least the -3 and -4 I get, L--->E however I dont get it! if you go "upper" you end up in L-P not L-E <===> upper left you use P-E , this I get, upper left is indeed E-P)
However the third one I dont get i!
Third computation is [Left] E ---> E = -1 + 1 (for match) = 0
==> where do you get "the match" from?
L and E do not match (I use the letters from the original square, not the letters from the "upper, upper-left or left" square like you seem to do)... You seem use the E from the left square ? Altough, I dont understand this, because you use the E from the left (left from 0); the E from the column left from the L. (and stay on the same row)

I dont see why you do this.

Is it because you need to use the letter from the square you refer to (I mean: left square, upper square, upper-left square) rather than the square itself you are trying to calculate?

[muthu545]

Hi Philie,

Sorry the making it more confused for you,
As you mentioned some of the values in the figure presented in the links are wrong

Imagine its a 2X2 matrix
-->E L
P -3 -4
E -1 X

This is the 2X2 matrix you need to consider..... X is the value you need to compute....
X is a combination of E--->L and this can be computed as explained below.

First computation is [Upper-left of X] which is comparing
P ---> E, the already present value is -3 and then E does not match
with L so you need to add -1... which will result in -4

Second computation is [Upper/above of X] which is comparing
P--->L = -4 + -1 (for mismatch of E and L) = -5
I had a mistake in this explanation, previously i mentioned it as L to E

Third computation is [Left of X] which is comparing
E ---> E = -1 + -1 (for mismatch of E and L) = -2

Thanks, sorry again
--
Muthu

[phillie]

Hi, yes are right, "you need to use the letter from the square you refer to (I mean: left square, upper square, upper-left square) rather than the square itself you are trying to calculate"

Imagine its a 2X2 matrix
-->E L
P -3 -4
E -1 X

This is the 2X2 matrix you need to consider..... X is the value you need to compute....
X is a combination of E--->L and this can be computed as explained below.

First computation is [Upper-left of X] which is comparing
P ---> E, the already present value is -3 and then P does not match
with E so you need to add -1... which will result in -4

Second computation is [Upper/above of X] which is comparing
P--->L = -4 + -1 (for mismatch of P and L) = -5
I had a mistake in this explanation, previously i mentioned it as L to E

Third computation is [Left of X] which is comparing
E ---> E = -1 + 1 (for match E matches with E) = 0


Note that We are trying to align two strings
'PELICAN' and 'COELACANTH' and try to find the best
alignment possible.

Thanks
--
Muthu

Ok
lets say your reasoning is correct.
Than take column C (second C) (-6) and row C ==> its a 0 there..
Using your logic this can never be 0 !
Upper= C and I
Left = A and C
upper left = A and I

I dont think you need to use the letter from the upper/upper-left or left ...

If you dont ==> C and C match, than I can see how they get the 0 (upper left = -1 + 1 = 0)

Also: I dont really see it writen in the webpage you need to use the letter from the upper/upper-left or left square... Shouldnt they state this because this is pretty important...

[muthu545]

I agree with you, philie.... Some of the values are wrong in the figure.
As you mentioned in your first post the value for E-->L cell should be -2.
I updated my previous post.


Thanks
--
Muthu

[phillie]

I agree with you, philie.... Some of the values are wrong in the figure.
As you mentioned in your first post the value for E-->L cell should be -2.
I updated my previous post.


Thanks
--
Muthu

Oh ok.

Well I was confused because if seemed to contain errors... but than I started to think it was on a "nature" website and from a book.. I found it weird to contain so many mistakes.. so I started to doubt myself.

But since you agree too.. I guess the people that wrote this made an error.

[muthu545]

Hi Phillie,

The actual figure in the print should look like the following


The # in red color are the right numbers.

Hope this makes it clear.

I think while they are formatting the figure for the print, they added -ve signs to all the cells and interchanged few cells.

Thanks
--
Muthu

[phillie]

Hi Phillie,

The actual figure in the print should look like the following


The # in red color are the right numbers.

Hope this makes it clear.

I think while they are formatting the figure for the print, they added -ve signs to all the cells and interchanged few cells.

Thanks
--
Muthu

AHa!
thats seems better.
I'll check it.
Too bad , at first sight, I cant find more than just that picture, rather than a website explaining it more.
But this will help already.
thanks a lot.