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?



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.

  • $\begingroup$ The Altschul article is definitely what you should look at as it's on the BLAST website. There is one relevant section entitled: "The choice of substitution scores" and another entitled "The PAM and BLOSUM amino acid substitution matrices". Have fun digesting them! $\endgroup$
    – David
    Apr 16 '16 at 20:39

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