By Paul Barry, Michael Moorhouse
Bioinformatics, Biocomputing and Perl offers a latest creation to bioinformatics computing abilities and perform. Structuring its presentation round 4 major parts of research, this ebook covers the abilities very important to the daily actions of today’s bioinformatician. every one bankruptcy incorporates a sequence of maxims designed to spotlight key issues and there are routines to complement and cement the brought material.
Working with Perl offers a longer educational creation to programming via Perl, the prime programming know-how of the bioinformatics group. although no prior programming event is believed, finishing the educational equips the reader being able to produce robust customized courses very easily.
Working with Data applies the programming talents bought to processing various bioinformatics info. as well as suggestion on operating with vital facts shops reminiscent of the Protein DataBank, SWISS-PROT, EMBL and the GenBank, significant dialogue is dedicated to utilizing bioinformatics info to populate relational database systems. the preferred MySQL database is utilized in all examples.
Working with the Web offers a dialogue of the Web-based applied sciences that permit the bioinformatics researcher to post either information and purposes on the net.
Working with Applications shifts apparatus from growing customized courses to utilizing them. The instruments defined contain Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An creation to the $64000 Bioperl undertaking concludes this bankruptcy and rounds off the booklet.
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Extra resources for Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice
When ‘‘$count % 2’’ yields zero, the word ‘‘even’’ is printed, and when ‘‘$count % 2’’ yields anything other than zero, the word ‘‘odd’’ is printed. 40 The Basics The oddeven2 program is shorter than oddeven. But is this enough to make it better? On its own, it is not. However, the oddeven2 program is better because it is easier to extend. Speciﬁcally, if the program is changed to iterate 20 times, we need only make one change: the value for HOWMANY becomes 20 instead of 4. Contrast this to the changes required to the oddeven program: adding 16 new elsif blocks for each of the new values of $count, 4 through 19.
Bioinformatics! Bioinformatics! Bioinformatics! Bioinformatics! The forever program repeatedly prints the message on screen, and it continues to print the message while TRUE is true. So the program runs forever. The Ctrl-C key combination must be pressed to stop the program executing. Technical Commentary: Rather than use the word iteration or repetition to refer to this mechanism, many programmers favour the use of the word loop. In this context, loop is both a noun and a verb. Typical programmer utterances might be ‘‘the loop prints the message ﬁve times’’ or ‘‘this program loops forever’’.
Returning to the getlines program, note that the <> operator returns a line from standard input and assigns it to $line. The trueness of the $line scalar is then tested. If $line contains one or more characters it is considered to be true, otherwise it is considered to be false. That is, if it contains no characters, it is an empty string, and ‘‘empty’’ implies false. Obviously! Remember the earlier warning in this chapter that Perl had its own unique notion of truth. So, the loop in getlines keeps iterating while there are lines of input arriving from standard input, that is, the keyboard.