Youre right. Ive been using this example to test my alignment function and ive came to the same conclusion. Theyve made a couple of mistakes and as such, most of the lower triangle, as well as C-Y pair you mention, is incorrect.
I'm not sure about what you mean, Ankit. These matrices are in built in sequence alignment tools like BLAST and Clustal Omega . So you take a sequence or sequences of your choice and go to say BLAST...then in the parameters section one can choose the type of matrix used for alignment.
Did I just see you fudge the matrix numbers toward evolutionary theory? "Evolutionary theory is 'implicit' in the alignment theory." Guess there was maybe too much obvious about the old theory where evolution was 'explicit'. What happens to the alignments if you don't fudge? Does evolution become too improbable? Scientific, huh? You sure had a lot of explaining to do to justify that 250% crap to get your alignments. You didn't even seem to convince yourself.
Quentin McClaran What he was saying, is that your scoring mechanism carries with it an implicit model of mutation. It seems you didn't understand the lecture, the 3rd grade is that
It is impossible to perform any alignment that is not a perfect match without some evolutionary assumption. Consider the alignment here: en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm#Gap_penalty How could you favor one alignment over the other without a biological model describing the relative probability of an insertion or substitution?
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Great lecture!
In 1:00:35: Shouldn't that C-Y in (5,5) be 5 instead of 3 as we can come from 13 with a gap penalty of -8, i.e., 13-8=5?
Also in E-V in (1,1) we will get -4 as we come down from 4 as a gap penalty.
You mean E-V in (1, 2) right? I've noticed the same thing, but I'm not sure if it's actually a mistake or if we're just missing something...
Youre right. Ive been using this example to test my alignment function and ive came to the same conclusion.
Theyve made a couple of mistakes and as such, most of the lower triangle, as well as C-Y pair you mention, is incorrect.
can you help me how to find the PAM 250 matrix or show me the step of how to find PAM 250 matrix?
I'm not sure about what you mean, Ankit.
These matrices are in built in sequence alignment tools like BLAST and Clustal Omega .
So you take a sequence or sequences of your choice and go to say BLAST...then in the parameters section one can choose the type of matrix used for alignment.
All the information you need is in the "Understanding bioinformatics" textbook. Hope this comment is still useful for you.
thx
Did I just see you fudge the matrix numbers toward evolutionary theory? "Evolutionary theory is 'implicit' in the alignment theory." Guess there was maybe too much obvious about the old theory where evolution was 'explicit'. What happens to the alignments if you don't fudge? Does evolution become too improbable? Scientific, huh? You sure had a lot of explaining to do to justify that 250% crap to get your alignments. You didn't even seem to convince yourself.
Quentin McClaran What he was saying, is that your scoring mechanism carries with it an implicit model of mutation. It seems you didn't understand the lecture, the 3rd grade is that
It is impossible to perform any alignment that is not a perfect match without some evolutionary assumption. Consider the alignment here: en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm#Gap_penalty How could you favor one alignment over the other without a biological model describing the relative probability of an insertion or substitution?