Errata

Developing Bioinformatics Computer Skills

Errata for Developing Bioinformatics Computer Skills

Submit your own errata for this product.

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 Note Update

Version Location Description Submitted by Date submitted
Printed Page 1
Chapter 1

I read the example chapter online, it's Chapter 1 but there are no page numbers.
Here's the phrase: "With a commonly used computer program called fsBLAST". There's no
such thing as a program called fsBLAST, it's BLAST.

 Anonymous   
Printed Page 7
middle line between two sequence alignments "Query: 24" and "Sbjct: 17"

In the book's first visual display of a sequence alignment on page 7, the
middle line showing the relationship between the eyeless gene and the aniridia
gene is formatted two spaces too far to the left so that HSGVNQLGGVFV
GRPLPDSTRQKIVELAHSGARPCDISRILQVSN, which should begin at base pair 15, starts
at base pair 13. This error could be rather confusing to someone who had
little experience with sequence alignments and didn't pick up on the error,
since in the text it explicitly says, "If there is a letter on the middle
line, the sequences match exactly at that position... If there is nothing on
the middle line, the two sequences don't match at that position." Yet due to
the formatting error, this statement is no longer true on the first line of
the alignment, though it should be.

Anonymous   
Printed Page 11
Figure 1-3

The marker for "The Origin of Life" (presumably the Last Common Ancestor) is indicated to be between Eukaryotes and Archaea, but should be moved to the right of Archaea to indicate that it preceeds the split from eubacteria. Eukaryotes and Archea are thought to be more closely related to each other than to eubacteria and all three have the origin of life in common as prokaryotic common ancestor.

 Anonymous  Nov 18, 2008 
Printed Page 25
last paragraph

This section is about the translation of mRNA to protein, yet this
paragraph says, "...the genetic code is the code that translates DNA into
protein" and "it takes three bases of DNA...". It goes on to say, "Figure
2-4 shows how RNA is translated into protein". There seems to be confusion
about whether DNA or mRNA or RNA is translated into protein.

 Anonymous   
Printed Page 26
Figure 2-4

tRNA translation of GAU is shown as mapping to Gly, yet figure 2-3
shows GAU as mapping to Asp. This may confuse someone who is not
familiar with the Genetic Code.

 Anonymous   
Printed Page 36
1st paragraph, last sentence

The word "protein" begins the sentence and should be capitalized: "Protein structure alignment tools are introduced in Chapter 10."

 Anonymous   
Printed Page 56
JDK/JRE;

The text reads

"to use Java-based tools such as the Jalview sequence editor we
discuss in Chapter 4, Files and Directories in Unix."

Jalview is discussed in Chapter 8 (page 196).

 Anonymous   
Printed Page 67
3rd paragraph

The directory "home/jambeck/mustelidae" should be changed to
"/home/jambeck/mustelidae"


 Anonymous   
Printed Page 74
long format of ls (code)

"Mar5" should be changed to "Mar 5"

(chapters 3, 4, 5) all;
Recurring inconsistencies:

The authors do not differentiate between a file and a filename. Pages 100, 101,
102, and 103: in the Usage parts, they use "file", "files", "filename",
"filenames", and even "filename(s)" on page 109.

 Anonymous   
Printed Page 95
seventh paragraph

"meercat.txt" doesn't exist. It should be changed to "meercat10.txt".

 Anonymous   
Printed Page 98
Status line

It is a colon (:) not a semicolon (;) that is used to get to the
status line in vi. The error occurs twice in the first paragraph
on page 98.

 Anonymous   
Printed Page 99
2nd list item

"r]" should be ":r"

 Anonymous   
Printed Page 101
last section

"- number" should be "-number"

 Anonymous   
Printed Page 102
3rd paragraph

"num" should be "number"

 Anonymous   
Printed Page 103
second half

If you use cut -f 1-2 sequence_data on the described file, you will get
both fields (both columns) send to stdout, at least you will get ATC TAC
(the first line) but never AAT TAC, will you?

 Anonymous   
Printed Page 103
command line example after 3rd paragraph

the csplit example

%csplit -f dbrecord. -n 6 fastadbfile /^>/

splits the input file just in two parts, splitting at the first occurence of ">".

to split the input file into many single sequence files the option
"{*}" has to be added

(confirmed with csplit from GNU textutils 2.0.11)

 Anonymous   
Printed Page 110
options

--help and --version are usable for all the given commands. Why did the
authors specifically add it here ?

 Anonymous   
Printed Page 112-3
last paragraph

The amino acid sequence in the seqres file starts at 14 and ends at 64, so
that the command must be: cut -c14-64 seqres > seqs to get the output shown
on toop of the next page. This is a little bit inconsistent and confusing,
like the known error on page 7.

BTW: the same numbering error occurs on page 104 in the piped command "%
grep SEQRES pdbfile| cut -c...."

 Anonymous   
Printed Page 113
script

The temporary file is not removed, and since authors are dealing within
GenBank files (several Mb at a time), they really need to remove it in the
foreach loop. This is a major issue.

Also, there isn't any indentation: if you want biologists to develop computer
skills, you have to explain to them how to indent scripts and Perl programs.

 Anonymous   
Printed Page 115
first paragraph

The directory "/home/httpd/html" is too specific. It would be better explain
things using httpd.conf and grep '^ServerRoot' in this file to obtain the
appropriate directory.

 Anonymous   
Printed Page 115
Usages

inconsistencies: telnet full.hostname and ftp full.host.name.edu

Anonymous   
Printed Page 115
ftp section

"The File Transfer Protocol (ftp)" should be "The File Transfer Protocol
(FTP)". ftp is a program. FTP is the protocol.

 Anonymous   
Printed Page 116
3rd paragraph from the bottom


% xhost +

is an inappropriate command. It should be:

% xhost +remote_hostname

to prevent potential security problems.

 Anonymous   
Printed Page 120
3rd paragraph

Can you briefly explain this sentence:

Even on a single processor system, it's possible to have multiple
processes running concurrently as long as there is enough space for
both jobs to remain in memory.

I am not sure of what you really mean.

 Anonymous   
Printed Page 122
list of top options

"-d" should be "-d delay"

 Anonymous   
Printed Page 123
last paragraph

Since priority value is in range 1-19, writing "but unless you are root,
you are limited to raising its priority to 1" doesn't make sense.

 Anonymous   
Printed Page 126
last paragraph

/zeus: should be zeus:

 Anonymous   
Printed Page 134
5th paragraph

If you search for protein structure on Excite....
^^^^^^^
Google defaults to AND, so you'll find only references that
contain protein and structure....
^^^^^^^ ^^^^^^^^^

The indicated words should be in italic.

 Anonymous   
Printed Page 142
3rd paragraph; The first sentence

Reads:

The standard reduced representation of the 3D structure of biomolecule
consists of....

It should read:

The standard reduced representation of the 3D structure of biomolecules
consists of....

 Anonymous   
Printed Page 154
1st paragraph, 2nd sentence

The forward reference promising to discuss the differences between PDB and mmCIF in Chapter 12 is not kept. Checking the index, neither PDB nor mmCIF has any entries between pages 331 and 349 -- all of Chapter 12. Actually reading through the chapter confirms that neither of those formats are discussed in the course of the chapter. Similarly scanning through the pages where "mmCIF" appears (according to the index) does not give me any further details about differences between the two, other than that mmCIF is newer and the 'community is still attached' to PDB.

 Anonymous   
Printed Page 160
Bottom paragraph

The last sentence reads:

But keep this fact in mind: the single-letter sequence code
that describes DNA and is a simplified representation....

It should read:

But keep this fact in mind: the single-letter sequence code
that describes DNA is a simplified representation....

Anonymous   
Printed Page 216
Section: A Word About.... 1st paragraph, last sentence

The sentence promises to give an example of file-format conversion in Chapter 12. The examples in Chapter 12 deal with string/pattern searching/matching and parsing BLAST data to compile a report. If the BLAST parsing is the intended example, some other phrasing should be used instead of "file-format conversion" on page 216. Most anyone reading those words will think something similar to converting GIF to JPEG (image formats) rather than what's actually provided in Chapter 12. Or perhaps the example was omitted at printing and the reference to it here and elsewhere was not also removed?

 Anonymous   
Printed Page 218
Figure 9-1

N should be H on C with R2

 Anonymous   
Printed Page 236
2nd full paragraph, line 2

"forwRasMolard" should be "forward".

 Anonymous   
Printed Page 245
5th paragraph - section CATH

The URL for CATH sould read

http://www.biochem.ucl.ac.uk/bsm/cath_new/

(original is missing the ucl portion of the hostname)

 Anonymous   
Printed Page 246
last paragraph

You mention that you do not know of any software that allows a user to "create
a unique data set based on your own choice of parameters".

Actually, our website does allow this. There is a form where one can choose
resolution, sequence identity, R-factor, length cutoffs as well as whether to
include C-alpha only or NMR structures.

The website address is:

http://www.fccc.edu/research/labs/dunbrack/culledpdb.html

 Anonymous   
Printed Page 294
2nd paragraph, 2nd to last sentence

"pheotype" should probably be "phenotype"

 Anonymous   
Printed Page 301
2nd paragraph

The text at the end of paragraph 2 states: ...the fragment of a genome can be ordered
into a highly specific map (see figure 11-2).

Figure 11-2 (page 298) however is the detector output for modern sequencing
experiment, and not show a figure of a highly specific map. Other figures in this
chapter also do not fit this description, so it looks like a figure is missing from
the book .

 Anonymous   
Printed Page 324
3rd paragraph

Where would one locate PATH-DB?

 Anonymous