Question

Alignment Matrix

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10.9 years ago

jan.shegers ▴ 10

Dear all,

I have a problem with the following website: http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast-29096

More specific, I have a problem with the matrix (completely filled in one). Is it possible that some errors have been made while completing this matrix? If you look (for example) at "the crossing" of row 4 and column 2 => L(-4) and E(-2), if I compare those, I do not get -0 as a score, I get -2 (-1 + -1 =-2)

So I am not sure if this matrix is filled in correctly or I am doing something horrible wrong here.

alignment blast • 2.0k views

ADD COMMENT • link updated 10.9 years ago by Giovanni M Dall'Olio 28k • written 10.9 years ago by jan.shegers ▴ 10

score 2 · Answer 1 · 2013-05-28

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10.9 years ago

Devon Ryan 104k

Yes, there appear to be a number of errors there (I counted 6, but may have missed some). Googling around a bit, it seems that this is a known problem. The graphic was from a book, for which there is an update image.

ADD COMMENT • link 10.9 years ago by Devon Ryan 104k

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Complete disregard for computational methods in a NPG publication? I don't believe it! ;)

ADD REPLY • link 10.9 years ago by Neilfws 49k

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+1 for the sarcasm

ADD REPLY • link 10.9 years ago by JC 13k

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Aha, ok I see. Thanks. I was doubting my approach.

ADD REPLY • link 10.9 years ago by jan.shegers ▴ 10