By James Tisdall
With its hugely built means to observe styles in information, Perl has turn into the most renowned languages for organic information research. but when you're a biologist with very little programming adventure, beginning out in Perl could be a problem. Beginning Perl for Bioinformatics is designed to get you quick over the Perl language barrier by way of drawing close programming as a tremendous new laboratory ability, revealing Perl courses and strategies which are instantly necessary within the lab. each one bankruptcy makes a speciality of fixing a selected bioinformatics challenge or type of difficulties, beginning with the easiest and extending in complexity because the publication progresses. every one bankruptcy contains programming workouts. through the tip of the ebook you'll have a pretty good realizing of Perl fundamentals, a set of courses for such initiatives as parsing BLAST and GenBank, and the talents to tackle extra complex bioinformatics programming.
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Extra resources for Beginning Perl for Bioinformatics
Concatenation is attaching something to the end of something else. A biologist is well aware that joining DNA sequences is a common task in the biology lab, for instance when a clone is inserted into a cell vector or when splicing exons together during the expression of a gene. Many bioinformatics software packages have to deal with such operations; hence its choice as an example. Example 4-2 demonstrates a few more things to do with strings, variables, and print statements. Example 4-2. /usr/bin/perl -w # Concatenating DNA # Store two DNA fragments into two variables called $DNA1 and $DNA2 $DNA1 = 'ACGGGAGGACGGGAAAATTACTACGGCATTAGC'; $DNA2 = 'ATAGTGCCGTGAGAGTGATGTAGTA'; # Print the DNA onto the screen print "Here are the original two DNA fragments:\n\n"; print $DNA1, "\n"; print $DNA2, "\n\n"; # Concatenate the DNA fragments into a third variable and print them # Using "string interpolation" $DNA3 = "$DNA1$DNA2"; print "Here is the concatenation of the first two fragments (version 1):\n\n"; print "$DNA3\n\n"; # An alternative way using the "dot operator": # Concatenate the DNA fragments into a third variable and print them $DNA3 = $DNA1 .
N is the common representation for "unknown," as when a sequencer can't determine a base with certainty. Later on, in Chapter 9, we'll need the other codes, for groups of nucleic acids, when programming restriction maps. Note that IT-SC 42 the lowercase versions of these single-letter codes is also used on occasion, frequently for DNA, rarely for protein. The computer-science terminology is a little different from the biology terminology for the codes in Table 4-1 and Table 4-2. In computer-science parlance, these tables define two alphabets, finite sets of symbols that can make strings.
Then compare each pair of bases as you read the two strands: they should always be paired C to G and A to T. Just by reading in a few characters from the starting DNA and the reverse complement DNA from the first attempt, you'll see the that first attempt at calculating the reverse complement failed. It was a bad algorithm. This is a taste of what you'll sometimes experience as you program. You'll write a program to accomplish a job and then find it didn't work as you expected. In this case, we used parts of the language we already knew and tried to stretch them to handle a new problem.
Beginning Perl for Bioinformatics by James Tisdall