programming-for-dummies

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Bioinformatics Programming
Although you could type molecular sequences by hand, it’s far easier to let
the computer do it for you, especially if you want to compare a large number
of sequences with BLAST. After BLAST gets through comparing your
sequences, it returns a list of matching sequences.
Using BLAST to compare sequences to a database of known sequences is an
example of data mining. (See Chapter 1 of this mini-book for more information
about data mining.)
You could scan through this list of matching yourself, but once again, that’s
likely to be tedious, slow, and error-prone. Writing a program that can parse
through reports generated by BLAST to look for certain characteristics is
much simpler. Essentially, you can use the computer to automate sending
data to BLAST and then have the computer filter through the results so you
see only the sequences that you care about.
Now you could write another program to skim or parse through the database
results to filter out only the results you’re looking for. Because every
database stores information in slightly different formats, you might need to
write another program that converts file formats from one database into
another one.
Because every biologist is using different information to look for different
results, there’s no single bioinformatics program standard in the same way
that everyone has flocked to a single word processor standard, like Microsoft
Word. As a result, bioinformatics involves writing a lot of little custom programs
to work with an ever-growing library of standard programs that biologists
need and use every day.
Some biologists can learn programming and do much of this work themselves,
but it’s far more common for biologists to give their data to an army of bioinformatics
technicians who take care of the programming details. That way the
biologists can focus on what they do best (studying biology) while the programmers
can focus on what they do best (writing custom programs). The
only way these two groups can communicate is if biologists understand how
programming can help them and the programmers understand what type of
data and results the biologists need.
Bioinformatics Programming
Because biologists use a wide variety of computers (UNIX, Windows, Linux,
and Macintosh), they need a programming language that’s portable across
all platforms. In addition, biologists need to work with existing programs,
such as online databases. Finally, because most biologists aren’t trained as
programmers, they need a simple language that gets the job done quickly.