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Why does the score matrix influence the E value (BLAST)

Why does the score matrix influence the E value (BLAST)


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When I align two HBB protein sequences wich have 80% identity, I used two kind of score matrices: Blosum62 and PAM30, to figure out the impact on my results.

I noticed that the bit score is higher when I used PAM30 instead of BLOSUM62, which makes sense because PAM30 is based on more closely related species.

However I don't understand why the E-values differs from each other:

PAMP62: Bit score: 251, E value: 8 * 10^91

PAM30: Bit score: 258, E value: 6*10^82

Question: I don't understand why the E-value changes when using an other scoring matrix?

thankyou,


Perhaps this BLAST tutorial by Steve Altschul will be helpful: The Statistics of Sequence Similarity Scores

There is also the BLAST book by Mark Yandell and Ian Korf.


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Comments:

  1. Corwine

    Informative, but not convincing. Something is missing, but what I don’t understand. But, let me tell you straight: - bright and benevolent thoughts.

  2. Alvaro

    wonderfully, is the phrase very valuable

  3. Jeffery

    It cannot be!

  4. Thorn

    the idea Excellent and timely



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