Bioinformatics is

1
Bioinformatics is

• - the use of computers and information
  technology to assist biological studies
• - a multi-dimensional and multi-lingual
  discipline

Chapters 1-4, Tisdall
2
Multiple platforms, multiple languages

• Windows, Mac, UNIX, Linux
• UNIX remains the standard for bioinformatics
  software development, while PCs and Macs are
  typically end-users.
• Java, Python, CORBA, C, Ruby, Perl
• Theres more than one way of doing things.
• Uniformity continues to be one of the biggest
  problems faced in bioinformatics

3
Why Perl?

• Ease of use by novice programmers
• Fast software prototyping
• Flexible language
• Compact code (sometimes)
• Powerful pattern matching via regular
  expressions
• Availability of program and modules (BioPerl)
• Portability
• Open Source easy to extend and customize
• No Licensing fees

4
Perl is easy to get

• Many computers come with Perl already installed
• Check by typing perl v in a Unix, Linux, MacOSX
  shell, or Windows MS-DOS shell
• If not, simply go to www.perl.com, or
  www.activestate.com to download a recent version
  of Perl (download binary whenever possible,
  source code requires compiling)
• ActiveState provides several tools for Perl
  developers (Although some think Perl is an old
  language, it is constantly undergoing revision
  and improvement

5
What is Perl?

• Practical Extraction Report Language
• An interpreted programming language optimized for
  scanning text files, extracting information, and
  printing reports
• The string-based language of DNA and protein
  sequence data makes this an obvious choice

6
What is a Perl program?

• A program consists of a text file containing a
  series of Perl statements
• Perl programs can be written in a variety of text
  editors including MS Word, WordPad, NotePad, or
  as you will use Komodo from ActiveState
• Perl statements are separated by semi-colons ()
• Multiple spaces, tabs, and blank lines are
  ignored
• Anything following a is ignored (comment line)
• Perl is case sensitive

7
Perl has three data types

• - Scalar holds a single value, which can be a
  number or string, EcoRI GAATTC
• _at_ - Array stores multiple scalar values 0, 1,
  2, etc.
• - Hash An associative array with keys and
  values

8
Using Scalar Variables

• Example 4-1 Tisdall provides a simple example, a
  thorough description of this exercise is supplied
  both in the text

9
Some additional comments regarding strings

• Quotes
• XYZ Text between a pair of single quotes is
  interpreted literally
• To get a single-quote in a string precede it by a
  backslash
• To get a backslash into a single quoted string,
  precede backslash with backslash
• hello hello
• can\t cant
• http\\\\www http\\www

10
Double quotes interpolate variables

• variable names within the string are replaced
  by their current values
• x 1
• print x will print out x
• print x will print out 1

11
Arithmetic operators

• Addition
• - Subtraction
• Multiplication
• Exponentiation
• / Division
• Modulus

12
Other important operators

• is an assignment operator
• or eq is equals
• or - assignment operators that add or
  subtract, a 2 means a a 2
• ,, -- are autoincrement operators that add or
  subtract one from variable when following
  variable (a a 1)

13
\n newline

• Often times you would like to introduce some
  spacing into your output
• \n introduces a blank line following any variable
  
• Print apple
• print grape
• Output looks like apple
• grape
• Print apple\n
• print grape\n
• Output looks like apple
• grape

14
Chomp and Chop

• Chop removes the last character from a string
• a Dr. Barber is hip
• Chop (a) a is now Dr. Barber is hi
• Chomp removes a line from the end of the string
• a Dr. Barber is hip\n
• Chomp (a) a is now Dr. Barber is hip

15

• Do examples 4-2, 4-3, 4-4

16
Working with Files
Biological data can come in a variety of file
formats and our job is to utilize these files and
extract what we want One such file format is
FASTA
17
Scalar vs. Array

• Example 4-5 provides a simple distinction between
  use of a scalar variable and an array, read it,
  but dont necessarily do it
• Also, it shows how you use filehandles in
  association with your file
• lt gt are input operators, you will become better
  acquainted with this when we use ltSTDINgt later

18
adhI.pep

• Supplant NM_021964fragment.pep with adhI.pep,
  which can be downloaded from the web-site to a
  folder you need to create on your computer called
  BIOS482
• Do Example 4-7, if time permits write analogous
  code to the code that follows this example to
  test out arrays