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# Computational Biology / Bioinformatics/Matrix allignment question

Question
Dear sir,

I am trying to undertand how matrix allignment works for the calculation of scores when comparing DNA sequences, however I stumbled upon a problem.
http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast

I use this webpage to understand how the allignment works.
However, when checking the matrix (fig 1E) I noticed some values seem wrong to me.
I do not understand how they calculated it.

For example:
horizontale speaking: L (4the letter from coelecanth) and the letter E (vertically, second letter of pelican) they give this a score of 0.
I do not get this.
FOllowing their reasoning, it would be a -2 according to me. Its not a match thus its -1 and the arrow points to the left, so it should be a -2 in total (-1 + -1)
Same goes for a few other numbers.

Dear Jan,
Actually different people use different method to explain the concept. The thing you are doing is actually focusing at one particular stage. But is should not be calculated like that. You have to consider the previous stage also. You can find more detailed explanation in the following link.

http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html

I hope it could solve your problem in understanding.

Computational Biology / Bioinformatics

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#### K Syed Ibrahim

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I can answer questions on Sequence analysis, Study materials. I cannot answer questions on Careers.

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8 years

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Ph.D., Biotechnology