By Paul Barry, Michael Moorhouse
Bioinformatics, Biocomputing and Perl offers a latest advent to bioinformatics computing talents and perform. Structuring its presentation round 4 major components of analysis, this booklet covers the abilities important to the day by day actions of today’s bioinformatician. each one bankruptcy features a sequence of maxims designed to spotlight key issues and there are workouts to complement and cement the brought material.
Working with Perl offers a longer instructional advent to programming via Perl, the prime programming expertise of the bioinformatics group. although no earlier programming adventure is believed, finishing the academic equips the reader having the ability to produce strong customized courses very easily.
Working with Data applies the programming talents bought to processing numerous bioinformatics facts. as well as suggestion on operating with vital information shops equivalent to the Protein DataBank, SWISS-PROT, EMBL and the GenBank, huge 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 let the bioinformatics researcher to post either facts and functions on the web.
Working with Applications shifts apparatus from growing customized courses to utilizing them. The instruments defined comprise Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An advent to the $64000 Bioperl venture concludes this bankruptcy and rounds off the e-book.
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Extra resources for Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice
However, try executing this command-line, which actually runs the program (note: the -c is missing): perl whoops And nothing appears on screen. Oh dear. The whoops program is semantically incorrect, in that it does not do what we were expecting it to do. In fact, it does nothing. The problem is that the 24 The Basics print command has been terminated too early. Look at that ‘‘;’’ character right after the word print in the program. What that tells perl is that the print command has ﬁnished printing.
However, its meaning is very different. We are asking perl to ‘‘sleep for one second’’, not to ‘‘sleep true’’, the latter being another example of syntactic correctness, but incorrect semantics. 3 More Iterations Iterating forever is occasionally useful. However, it is more common for iterations to execute for a speciﬁc number of occurrences. The loop in the forever program kept going while the value of TRUE remained true, which meant that forever was designed never to stop6 . The thing to check at the top of the loop has a generic name: condition.
It is often useful to determine the size of an array, where ‘‘size’’ refers to the number of elements currently in the array. 2 The grown @list of sequences array. \n"; When executed by perl, both statements display the following message on screen: The array size is: 4. When the name of the array is preﬁxed with ‘‘$#’’, the value returned by perl is equal to the largest array index associated with the named array. The largest array index for the @list of sequences array is 3. Array indexes are numbered from 0, so 1 is added to the $# value to calculate the number of elements in the array, which is 4 in this case.
Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice by Paul Barry, Michael Moorhouse