Beginning Perl for Bioinformatics
by  James Tisdall

The following errata were *corrected* in the 9/04 reprint:

Here's a key to the markup:
	[page-number]: serious technical mistake
	{page-number}: minor technical mistake
	<page-number>: important language/formatting problem
	(page-number): language change or minor formatting problem



[2] +3
of DNA and positions

NOW READS:
of DNA and proteins


[2] -3
as in translating it to RNA

NOW READS:
as in transcribing it to RNA


[3] +3  
Genbank, the Genetic Sequence Data Bank (http://www.ncbi.n/m.nih.gov)

NOW READS:
GenBank, the Genetic Sequence Data Bank (http://www.ncbi.nlm.nih.gov)


[3] -2
are composed of an amino group and a carboxyl group.

NOW READS:
are composed of an amino group, a carboxyl group, and a sidechain.


[14] -3 
type /my_program

NOW READS:
type ./my_program


[66] +2
(as was true in Example 4-3)

NOW READS:
(as was true in Example 4-5)



[74] Output from Example 5-4   
T = 17

NOW READS:
T = 17
errors = 1



[77] +2
This version of the foreach loop:

	foreach(@DNA) {.

NOW READS:
This version of the foreach loop:

	foreach (@DNA) {



[77] +2 
in the version of this loop in Example 5-5

NOW READS:
in the version of this loop in Example 5-4



[80] +1 (output of Example 5-6)
recognize this vase:

NOW READS:
recognize this base:


[81] +5
"seeing.
"

NOW READS:
"seeing".



[82] +1 (in code fragment)
# Also write the results to a file called "countbase"

$outputfile = "countbase";
(
unless ( open(COUNTBASE, ">$outputfile") ) {

NOW READS:
# Also write the results to a file called "countbase"
$outputfile = "countbase";

unless ( open(COUNTBASE, ">$outputfile") ) {




[82] footnote
several other behaviors.

NOW READS:
several other behaviors, such as appending to a file.


[93] warning
such as the my construct.

NOW READS:
with the my construct.  (Unless you're
using global variables, which we're not.)


[96] +4 code fragment
    AAGGGGTTTCCC

NOW READS:
    % perl example6-3.pl AAGGGGTTTCCC


[124] +4
greater than 0 and less than 7

NOW READS:
greater than or equal to 0 and less than 7


[149] +2
different data structures (hashes, arrays, and databases) can store

NOW READS:
different data structures (like hashes and arrays) and database systems can store


[156] +4
The chart in Figure 8-1 shows how the various bases combine to form amino acids.

NOW READS:
Figure 8-1 shows each codon and its associated amino acid: the genetic code.



[156] -2
the process stops when a codon is encountered.

NOW READS:
the process stops when one of the three stop codons is encountered.



[171] -1
It's convenient to declare these my variables as $line on the spot,

NOW READS:
It's often convenient to declare a loop's "index variable" (like $line)
as a my variable, right on the spot in the loop,


[176] Code for subroutine "revcom"
my($revcom) = reverse($dna);

NOW READS:
my $revcom = reverse $dna;