BLAST

This is the Title of the Book, eMatter Edition

Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.

64

|

Chapter 4: Sequence Similarity

Sequence Similarity

Sequence similarity is a simple extension of amino acid or nucleotide similarity. To

determine it, sum up the individual pair-wise scores in an alignment. For example,

the raw score of the following BLAST alignment under the BLOSUM62 matrix is 72.

Converting 72 to a normalized score is as simple as multiplying by lambda. (Note

that for BLAST statistical calculations, the normalized score is λS – lnk.)

Query: 885 QCPVCHKKYSNALVLQQHIRLHTGE 909

+C VC K ++ L++H RLHTGE

Sbjct: 267 ECDVCSKSFTTKYFLKKHKRLHTGE 291

Recall from Chapter 3 that the score of each pair of letters is considered indepen-

dently from the rest of the alignment. This is the same idea. There is a convenient

synergy between alignment algorithms and alignment scores. However, when treat-

ing the letters independently of one another, you lose contextual information. Can

you assume that the probability of A followed by G is the same as the probability of

G followed by A? In a natural language such as English, you know that this doesn’t

make sense. In English, Q is always followed by U. If you treat these letters indepen-

dently, you lose this restriction. The context rules for biological sequences aren’t as

strict as for English, but there are tendencies. For example, low