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The errata list is a list of errors and their corrections that were found after the product was released.

The following errata were submitted by our customers and have not yet been approved or disproved by the author or editor. They solely represent the opinion of the customer.

Color Key: Serious Technical Mistake Minor Technical Mistake Language or formatting error Typo Question



Version Location Description Submitted By
Printed Page 47
Figure 3.6

Local Alignment: Smith-Waterman

Error: Running Blast_example3-2.pl returns a different alignment matrix to the one
displayed in fig 3.6. Iterating through the score and pointer data returns the
following matrices:

>perl Blast_example3-2.pl COELACANTH PELICAN

1: 0 0 0 0 0 0 0 0 0 0
2: 0 0 1 0 0 0 0 0 0 0
3: 0 0 0 2 1 0 0 0 0 0
4: 0 0 0 1 1 0 0 0 0 0
5: 1 0 0 0 0 2 1 0 0 0
6: 0 0 0 0 1 1 3 2 1 0
7: 0 0 0 0 0 0 2 4 3 2
End Of Score Matrix..

1:0 0 0 0 0 0 0 0 0 0
2:0 0 0 0 0 0 0 0 0
3:0 0 0 - 0 0 0 0 0
4:0 0 0 | 0 0 0 0 0
5: 0 0 0 0 - 0 0 0
6:0 0 0 0 | - - 0
7:0 0 0 0 0 0 | - -
End Of Direction Matrix..

# The result is still the same
ELACAN
ELICAN

 Anonymous 
Printed Page 50
second paragraph`last sentence

O(n2) should be O(n^2) or "order n-squared"

 Anonymous 
Printed Page 56
top

equations for H are missing 1/p

 Anonymous 
Printed Page 58
equation 4-3

I think there should be parentheses around p_i*p_j so that the equation reads log(q_ij/(p_i*p_j))

Without them the equation as it stands is technically

log((q_ij/p_i)*p_j)

 Anonymous 
Printed Page 59
Fig. 4-2

Matrix is not 20 x 20. Valine is left out of rows. No way to finid out value of V to V.

 Anonymous 
Printed Page 59
Figure 4-2. Blosum62 scoring matrix

Missing last column coresponding to V aminoacid.

 Anonymous 
Printed Page 61
Equation 4-4

The Sum Sum_{i=1..n}Sum_{j=1..i} q_ij is not the sum of ALL frequencies it is only
the sum of the lower diagonal of the q_ij.
For example if n=4, then q_12 is not a member of the sum in the formula.

 Anonymous 
Printed Page 62
Equations 4-7, 4-8, 4-9

The j index should go from 1 to n, not from 1 to i. You want to sum ALL
scores, not just the lower diagonal ones. The example 4-1 in page 63 confirms this. If
you only sum the lower diagonal then $expected_socre = $match * 0.25 + $mismatch *
0.75 / 2.

AUTHOR: The equations are correct as they stand. The reason is that
in every case the value of xij is the same as xji. If you take both
halves of the diagonal then you are going to be off by a factor
of two.

 Anonymous 
Printed Page 62
Equation 4-9

According to Henikoff, S. and Henikoff J.G. 1992(http://www.pnas.org/cgi/reprint/89/22/10915.pdf), "H" should correspond to a measure of mutual information or relative entropy. It appears to me that there should not be a minus sign in front of right side summation. A relevant question is that "H" in this text may not necessarily be positive. In exceptional cases where there is no dependence between two matrices, "H" can be zero.

I think that relative entropy may not be the most suitable term to describe this equation, albeit being used in so many references about scoring sequence alignments. Relative entropy should be considered as a measure of the difference between two probability distributions, where mutual information, as expressed in the form of Equation 4-9, can be intuitively taken as a measure of dependence between two random variables. Scoring sequence alignments appears to correspond to the latter situation.

 Anonymous 
Printed Page 103
Figure 7-2

I have a question about the Sum score formula.

The summation runs from i = 1 to r. However, the individual S_i are not used in the summation. Only the constant S_r is used. i is not referenced anywhere in the summation.

Is this correct?

 Anonymous 
Printed Page 112
Code listing at bottom of page, 3rd paragraph

In the Perl Code listing, variable $n may be incorrectly commented:

'#actual length of query'

I think $n should be:

'# actual number of letters in database'

 Anonymous 
Printed Page 170
2nd paragraph, right below "Command-Line Tutorial"

The last part of the URL provided for the examples has "BLAST" in all upper case.

Turns out the URL is case sensitive, and this should be all lower case,
i.e., "9780596002992" to avoid the "404 Not Found" error.

 Anonymous 
Printed Page 173
10.3.1.5. 9780596002992x

9780596002992all -p blastx -d globins -i fugu_genomic > ncbi-blastx_test

should be:

9780596002992all -p blastx -d globins -i fugu_globin > ncbi-blastx_test

Anonymous 
Printed Page 215
second paragraph for CPUs and Computer Architecture

"Two benchmarks are provided Table 12-3." should be "Two benchmarks are provided Table 12-2."

 Jamming 
Printed Page 264
blastclust parameters

The reference for the important parameter "-S" is missing.
Score coverage threshold.

 Jamming 
Printed Page 310
line starting '$expect = "1$expect' ...

this line should be change FROM:
$expect = "1$expect" if $expect = ~/^e/;

... TO:
$expect = "1$expect" if $expect =~ /^e/;

the printed version will not correctly use your desired minimum expect value to filter the table entries.

 Anonymous