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Errata for first edition of Bioinformatics: Sequence and Genome Analysis

Chapter 1

Page 6 Figure 1.2 The vertical sequence "C A C T A G G C"
should read "G A C T A G G C"
Page 15 1st line "(2 X 109)" should read "(1.8 X 106)"

Chapter 2

Page 24
Last paragraph,
lines 4 - 5
"4-Mb" should read "1.8-Mb"
Page 40 3rd from last line "using the same two short sequences" should
read "using several short sequence fragments"

Chapter 3

Page 60
Figure 3.4
legend, last line
"sequences are identified" should read
"sequences are identical"
Page 61
2nd to last line "the lower left" should read "the lower right"
Page 69 Equation 1,
line 3
"Sij-y - wy" should read "Si,j-y - wy"
Page 70 Figure 3.9 legend,
part 1, last line
"upper right box" should read "upper left box"
Page 74 Line 11 "matched positions" should read "mismatched positions"
Page 87 Figure 3.15,
point 1, line 2
"other nine columns" should read "other nine positions"
Figure 3.15,
point 7, line 2
"-0.04" should read "-0.015"
"0.30" should read "0.15"
Page 91 Line 12 "may be obtained by multiplying the PAM1 matrix" should read "may be derived using Equation 4 after multiplying the mutation matrix in Table 3.4 by itself n times"
Page 104
Equation 16 "8.55" should read "8.99"
Page 107
Lines 13 and 22 "standard deviation" should read "variance"
Page 108
Line 6 "Combining Equations 25 and 27" should read "Combining Equations 22 and 27"
Page 111
Equation 37 "qi" should read "pj"
Line 38 "Equation 33" should read "Equation 36"
Page 119
Last line "P(A1 and B2)" should read " P(A2 and B1)"
Page 123
Line 10 "(~10 million to 4 billion years)" should read
"(~10 million to 4 billion years) times the prior
probability of each value of x"
Page 129
Figure 3.20
legend, 3rd to
last line
"right-hand corner" should read "lower
right-hand corner"

Chapter 4

Page 163 1st paragraph,
last line
"= 3.3" should read "= 3.3, which is converted to an integer to facilitate calculations"
Page 176 Table 4.2
Site column 1
"C" entry is "0.4", should read "0.2"
Line 1 "site starts is" should read "site starts there is"
Lines 4 and 5 "the first two nonsites, flanking background sequence positions, are 21 and 22" should read "the first two background sequence positions are 21 and 22"
Page 183 Line 5 "240 Gs" should read "216 Gs"
"10 X 80 = 800" should read "9 X 80 = 720"
Line 6 "fg, background = 240/800 = 0.30" should read
"fg, background = 216/720 = 0.30"
Page 185 Line 31 - 32 Website for SAM software should be "http://www.cse.ucsc.edu/research/compbio/sam.html", not "ucsd.edu"
Lines 36 and 42 "Figure 4.6" should be "Figure 4.16"
Page 186 Figure 4.16,
part B
The first purple circle labeled "D3" should be labeled "D1"
Page 187 Line4 "date" should be "data"

Chapter 5

Page 216 Figure 5.7A The horizontal axis label should be
identified as "j"
Figure 5.7B The red arrow in the upper right portion of
the panel should be extended

Chapter 6

Page 250 Figure 6.6 "Total tree length...1...2...3
plus 2 other charcter arrangements in trees II and III"
should read
"Tree length...1...2...2
plus 1 other character arrangement in tree II and 1 in tree III"
Figure 6.6 legend "Examples of phylogenetic analysis using the
maximum parsimony method" should read
"Examples of phylogenetic analysis based
on sequence position 5 in Table 6.3,
using the maximum parsimony method"
Page 256 Figure 6.11D The "2" to the left of the "C" should read
"1" and the "1" to the left of and above
the "D" should read "2"
Page 258 Example 2,
number 3
"Average distance between D and
ABC = d + m, m = g + [(c + 2f + a + b)/2]"
should read "Average distance between D and
ABC = d + m, m = g + [(c + 2f + a + b)/3]"
Page 260 14th from last
line
"sequences D and E in Example 2" should read
"sequences A and B in Example 2"
Page 266 Lines 6 - 7 "which corresponds to S, is then given by 1 - e-D such that" should read "which corresponds to 1 - S, is then given by 1 - e-D"
Equation 6 "S = 1 - e-D" should read "S = -e-D"
Page 276 Figure 6.22,
part A
There should be an asterisk above the sequences marking the column containing "T" "T" "A" and "G"

Chapter 7

Page 305 Figure 7.5 legend,
17th line
"(which is 10-36)" should read
"(which is 10-136)."

Chapter 8

Page 357 Lines 12 and 13 "SN is given by SN true positive/actual positives = TP/(TP+FN), the specificity by SP = true positives/predicted positives = TP/(TP+FP), and a correlation coefficient CC by"
should read
"SN is given by true positive/actual positives = TP/(TP+FN), the specificity by SP = true negatives/actual negative = TN/(TN+FP), and a correlation coefficient by"

Chapter 9

Page 386 Figure 9.2 legend,
4th to last line
"C=O group, also named C" should read "C=O group. An additional line to the end of the legend should read "The first carbon atom on the R group is named C."
Page 398 Table 9.3 label,
line 5
"resolution is 20 " should read "resolution
is 20 2"
Page 401 Table 9.4,
entry 5
Under Features, "minimation" should be "minimization"
Page 414 Figure 9.11 C "dendogram" should be "dendrogram" in sentences 2, 3, and 8
Page 418 Figure 9.13 labels on red line "Cα" and "Cβ" should read "Cα" only
Page 420 Figure 9.14 The heading "C. Summary matrix" should be
just above the graph that has "Protein A"
as a horizontal axis label
Page 445 line 2 "1720 = 14 X 1024" should read
"1720 = 4 X 1024"
Page 456 Example Last 4 lines should be moved to top of
Page 457
Page 467 3rd to last line
of text
"(see Fig. 9.2)" should read
"(see legend to Fig. 9.2)"

 

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