a link to the brain tumors you suspect exist.
->
a role in tumor development.

########################################

metaphor between the two disciplines.)
->
metaphor.)

########################################

Genbank
->
GenBank

## This is confirmed.

########################################

Genbank
->
GenBank

## This is confirmed.

########################################

itself or an adjunct to ongoing investigations.
->
itself, or as an adjunct to ongoing investigations.

########################################

and the computer program.
->
and computer programming.

########################################

large, programmable, digital/electronic (the ENIAC) computers.
->
large-scale, programmable, digital, electronic computers (such as ENIAC).

########################################

it's done so left to right
->
it's usually written left to right

########################################

It can appear as
->
It can appear in

########################################

most of the life
->
much of the life

########################################

easy to identify
->
easy to calculate the

########################################

such as the intriguing processes of
->
for instance, the intriguing techniques of

########################################

related by virtue of their protein products as part of
->
related by virtue of their protein products being part of

########################################

Mac, then
->
Mac, and then

########################################

several books such as O'Reilly's Perl Resource Kits,
->
several books

## The reader comments:
## I would suggest to remove "such as O'Reilly's Perl Resource Kits,".
## There is only the Win32 version still available, and even this version
## is totally outdated and much too expensive for the audience of this book.

## Tisdall says: sounds plausible to me: editors, how say you??

########################################

beginners, there's
->
beginners: there's

########################################

remember that
->
remember

########################################

perl example4 -1
->
perl example4-1

## This is confirmed.

########################################

more easily read
->
more easily readable

########################################

and to make sure
->
and its output to make sure that

########################################

to the right
->
on the right

########################################

new and successful way.
->
new and successful approach.

########################################

You can use any name
->
You can use any name for the file

########################################

both are listed in
->
both are demonstrated in

########################################

is assigned each time through the loop to
the next line of the file
->
is assigned to the next line of the file
each time through the loop

########################################

the type of input it gets.
->
the type of input the program gets.

########################################

Example 5-3, in Chapter 9, and
->
Example 5-3; in Chapter 9; and

########################################

characters, which is done globally
->
characters. This deletion is done globally

########################################

line, and a formfeed advances to the next line. The two of them
together amount to the same thing as a newline character.
->
line. Perl newlines are handled differently on different operating systems;
briefly,
works on all, but you may see
at the end of lines on Windows.

## This is confirmed.

########################################

We now have a design for the program, let's
->
Now that we have a design for the program, let's

########################################

is the same as previous
->
is the same as in previous

########################################

decimal or floating-point numbers
->
decimal (or floating-point) numbers
## italicise "floating-point"

########################################

or Perl documentation
->
or the Perl documentation

########################################

regularly
->
often

########################################

reading from, and writing to, files as well as other actions.
->
reading from files and writing to files, as well as other actions.

########################################

while($dna =~ /a/ig){$a++}
Should be:
while($DNA =~ /a/ig){$a++}

4th line from top;
$dna =~ /a/ig
should be:
$DNA =~ /a/ig

########################################

also has the global modifier,
->
also has the global modifier g,

########################################

you'll use those while loops to good effect
->
you'll use while loops in a similar fashion, to good effect

########################################

The program, however,
->
The program, moreover,

########################################

($dna = ~ tr/ACGTacgt//)
->
($dna =~ tr/ACGTacgt//)
There shouldn't be a space between = and ~

########################################

(eq actually an operator).
->
(eq is actually an operator).

## This is confirmed.

########################################

(Hint: you can use the Perl functions substr or slice.
->
(Hint: you can use the Perl functions substr or splice.)

## This is confirmed

########################################

mean of a distribution at
->
mean of a distribution, at

########################################

so-called recursion
->
## italicise "recursion"

########################################

The trick of all
->
The trick to all

########################################

We'll now look at this code
->
We'll now look more closely at this code

########################################

seen earlier in loops and conditional statements that groups
->
as the block used in a loop to group

########################################

You use the command line
->
You'll also use the command line

########################################

# Chapter Four, "Motifs and Loops"
->
# Chapter Five, "Motifs and Loops"

########################################

In the example of pass-by-reference in this section
->
In the example of pass-by-reference later in this section

########################################

passed on as arguments.
->
passed in as arguments.

########################################

appear in multiple program.
->
appear in multiple programs.

########################################

Beginning in Chapter 8, I'll define subroutines and show the code, but you'll be
putting them into your module and typing:
->
All the useful subroutines in this book will be put into this module, which
you'll start using in Chapter 8 by typing:

########################################

step you through that code as well.
->
steps you through that code as well.

########################################

The paragraph before the code:
"If you wish to see more lines, the w or "window" command will serve"
w adds a watch. It Should be v
"If you wish to see more lines, the v or "window" command will serve"

#######################################

Books states:

DB<12> D
Deleting all breakpoints..

But it should be:
DB<21> B *
Deleting all breakpoints...

#######################################

DB<13> w 45

Should it be
DB<13> v 45

######################################

Book states
DB<12> W $receivingcommittment

But should be w (lowercase)
DB<12> w $receivingcommittment

#######################################

Book
You see that at line 66 you misspelled

Should be
You see that at line 46 you misspelled

#######################################

Book states
"So fix the misspelling at line 66"

Should be
"So fix the misspelling at line 46"

#######################################

nonviable offspring that dies
->
nonviable offspring that die

########################################

they can lead to evolutionary
->
mutations can lead to evolutionary

########################################

the first and last sentences of this paragraph are redundant and one could be cut (I
would recommend cutting the last sentence).

first sentenct: "In the examples that follow, I use a simple Perl Method for seed
picking that's okay for most purposes."

last sentence: "In this book, I use a Perl method that is good enough for most
purposes."

######################################

that do the test first and then the block.
->
that test first and then do the block.

########################################

is really a short function
->
is a very short subroutine

########################################

It's just like the idea in
->
It's a subroutine to select a string position, very similar to the idea in

########################################

picking a random position then
->
picking a random position, then

########################################

have to do that a lot
->
have to look things up a lot

########################################

main program and proceeds, following the order of the
top-down design you did in pseudocode,
then followed by the subroutines.
->
main program and is followed by the subroutines,
in the same order as the top-down design you did in pseudocode.

########################################

nucleotide in the same position
->
nucleotides in the same positions

########################################

(indexed by $K)

should be
(indexed by $k)

########################################

Sometimes not all choices are will be picked
->
Sometimes not all choices are equally likely to be picked

## This is confirmed.

########################################

couldn't respond
->
couldn't respond informatively

########################################

You might try storing
->
You could store

########################################

in an array, for example, to search
->
in an array. For example, to search

########################################

databases. Some good ones that are free
->
databases, some good ones that are free

## This is confirmed.

########################################

Herein
->
Here

########################################

code, and the last subroutine clearly displays this redundancy.
It might be interesting to express that in your subroutine.
->
code, and subroutine codon2aa clearly maps several codons to the
same amino acid. We can represent this redundancy another way.

########################################

let's try to redo the subroutine
->
let's rewrite subroutine codon2aa

######################################

$codon
->
## could be formatted in nonproportional font

## Tisdall says: editors, how say you???

#######################################

condon2aa
->
codon2aa

## This is confirmed.

###########################################

"$codon = substr ($dna, $i 3);" should be
"$codon = substr ($dna, $i, 3);"

## This is confirmed.

########################################

biologists and programmers invented
->
biologists and programmers have invented

########################################

would think incorrectly, that the file
->
would think, incorrectly, that the file

########################################

As you accumulate useful subroutines in our modules,
->
As you accumulate useful subroutines in modules,

########################################

where in the DNA you're studying the cell
->
where, in the DNA you're studying, the cell

#########################################

## The equation should be reformatted so that:

+1
->
+ 1

#######################################

Pseudocode line near the bottom of the page, above last paragraph;
This is pseudocode, so it doesn't have to be perfect, but as written this line
looks like some kind of strange assignment instead of a comparison:

"(end - 1) - (start - 1) + 1 = end - start +1"

I'm not sure what the best way to fix this is. It is set in the monospace font
used for pseudocode & real code, but it isn't quite either, so I was going to s
uggest re-setting it in the variable width font used in the main text. That pro
bably won't clarify it either though, so the equals sign should probably just b
e doubled so that it's clear that the line is a comparison, and not an assignme
nt.

## Tisdall replies:
## This report is (kind of) confirmed. The line in question is an
## equation from elementary algebra.
## = as assignment in programming languages, and = as equality
## in algebra and much other mathematics, is indeed confusing
## (and has already been discussed), therefore let me add:

So let's write this subroutine:
->
as we know from algebra. So let's write this subroutine:

########################################

an.d
->
and

## This report is confirmed.

########################################

documentation (or Appendix B), for
->
documentation (or Appendix B) for

########################################

for each enzyme.To simplify matters
->
for each enzyme. To simplify matters

#######################################

the documentation on REBASE you found on its web site
->
the documentation from the REBASE web site

########################################

It's bad, because that same flexibility makes it harder to write programs that to
find and extract the desired annotations.
->
It's bad, because that same flexibility makes it harder to write programs that
find and extract the desired annotations.

## This is confirmed.

########################################

contains 12,813516 loci and
->
contains

########################################

(typical)) foreach{ ... } section of the parse1() subroutine, starting at
middle of page;
Most of the book's code is pretty clear & consistent, but one thing that the au
thor keeps wavering on is the inclusion or omission of spaces on lines like the
ones here. Appreviating, the code here has these lines:

} elseif( $in_sequence) {
} elseif ( $line =~ /^ORIGIN/ ) {
} else{

Note that the second elsif is followed by a space, but the first one isn't and
neither is the else. Likewise, $in_sequence has a leading space but not a trail
ing one.

## This report is correct. In this code fragment it does interfere with readability.
## Since the code is so dense here, I'd prefer:
if ( $line =~ /^//
/ ) {
}elseif ( $in_sequence ) {
}elseif ( $line =~ /^ORIGIN/ ) {
}else {
## But in general it's a deliberate choice to vary these things. 1) All such variations
## are legal Perl, and for good reason. 2) Beginners are likely to encounter such
## variations as they encounter different programming styles. 3) Beginners experiment
## with different styles as they develop their own preferences, so 4) I show the
## beginners different styles, and discuss the issue in the book.
##
## I am fully aware of the reason for standards for such formatting issues.
## However, I feel even in professional code they are not an unbreakable rule,
## and that readability is paramount. (You may feel that the only way to
## ensure readability is to follow a rule consistently, but I disagree.)

########################################

so that Perl doesn't interpret them as prematurely ending the pattern.
The regular expression also ends with a newline //
,
which is then placed inside the usual delimiters: ///
/
->
so that Perl doesn't interpret them as the usual / delimiters. The regular
expression is anchored to the beginning of the line (^),
ends with a newline (
), and is placed inside the delimiters: /^//
/

########################################

you can use another delimiter around the regular expression
->
you can replace the / delimiter with any character, like "!",

########################################

like so: m!//
!).
->
like so: m!^//
! where the expression is now ^//
).

#########################################

so it extends the ^ and the $
to match after, or before, a newline, embedded in the string.
->
so it extends the ^ to match after an embedded newline,
and the $ to match before an embedded newline.

########################################

First, let's examine
->
Let's examine

########################################

"I then saved the output as text in the file blst.txt, which is available from this..."
blst.txt
should be
blast.txt

########################################

the effect on biology and medicine would be profound.
->
the effect on biology and medicine will be profound.

########################################

you can give the directory name the special name "." for the current directory,
->
you can just call the directory by the special name ".",

########################################

given an scalar containing SEQRES lines,
->
given a scalar containing SEQRES lines,

## This is confirmed.

#######################################

In Chapter 10, I demonstrated two ways to parse GenBank files into sequence and
annotation and then how to parse the annotation into finer and finer levels of detail.
->
In Chapter 10, I compared two ways to parse GenBank files into sequence and
annotation, and to parse the annotation into finer and finer levels of detail.

########################################

what field the input line was in.
->
which section of the file each input line came from.

########################################

captures the pattern matched, denoted by $&
->
copies the pattern matched, denoted by the special variable $& that always holds
the last successful pattern match,

########################################

Let's examine the subroutine extractSEQRES, now that the record types have been
parsed out, and extract the primary amino acid sequence.
->
Now that the record types have been parsed out, let's examine the subroutine extractSEQRES,
and see how it extracts the primary amino acid sequence.

########################################

Our success with the previous parsePDBrecordtypes subroutine that used iteration
over lines (as opposed to regular expressions over multiline strings)
leads to the same approach here.
->
Our success in parsePDBrecordtypes using iteration over lines
(as opposed to regular expressions over multiline strings)
leads us to try the same approach here.

########################################

get_two__atoms
->
get_two_atoms

########################################

The actual running of the program and collecting its output happens in just one line.
->
The actual running of the program and collecting its output happen in just one line.

########################################

There are a several
->
There are several

########################################

before and after embedded newlines.
->
before and after embedded newlines, respectively.

########################################

FORTRAN programming-language conventions
->
FORTRAN programming language conventions

########################################

I've frequently mentioned modules and CPAN
->
I've frequently mentioned modules, and CPAN

########################################

the thousand of genes and gene products
->
the genes and gene products

########################################

Graphics programming language present
->
Graphics programming languages present

########################################