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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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