Bioinformatics: Computing Perspective

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BioinformaticsComputing Perspective

• Primary source
• Beginning Perl for Bioinformatics by James Tisdall

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Definition and Example

• text Bioinformatics is the application of
  computational tools and techniques to the
  management and analysis of biological data.
• example Does an interesting segment of mouse
  DNA hold a clue to the development of fatal brain
  tumors in humans?

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more on the example

• After sequencing the DNA, you search online data
  sources using web-based sequence alignment tools.
  This gives some related sequences but not a
  direct match to the suspected link to brain
  tumors. However, public genetic databases are
  growing daily at a rapid rate. Checking daily
  would be best, and Perl allow you to do so,
  comparing the results to detect changes and
  emailing you if there is a change.

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Wikipedia definition (en.wikipedia.org)

• Bioinformatics and computational biology involve
  the use of techniques including applied
  mathematics, informatics, statistics, computer
  science, artificial intelligence, chemistry, and
  biochemistry to solve biological problems usually
  on the molecular level. Research in computational
  biology often overlaps with systems biology.
  Major research efforts in the field include
  sequence alignment, gene finding, genome
  assembly, protein structure alignment, protein
  structure prediction, prediction of gene
  expression and protein-protein interactions, and
  the modeling of evolution.

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Organization of DNA

• DNA is polymer composed of four molecules (called
  bases or nucleotides)
• adenine (A) originally found in the glands
• cytosine (C) originally found in the cell
• guanine (G) originally found in guano
• thymine (T) originally found in the thymus
• Bases joined end to end form a single strand of
  DNA.

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More about DNA

• In the cell, DNA usually appears in a
  double-stranded form, with two strands wrapped
  around each other in a double helix shape. The
  two strands have matching bases, known as base
  pairs. An A on one matches with a T on the
  other, and a G is always paired with a C.
  Reverse complement is used to describe the
  relationship of the bases on the 2 strands.

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Biological study types

• in vitro means in glass (test tube)
• in vivo means in life (living organism)
• in silico refers to biological studies done on
  the computer
• Experimental data to be collected, searched, and
  analyzed usually requires the use of computers to
  manage the information. Computer simulation is
  another important tool in studying important
  biological problems.

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Perl

• Developed by Larry Wall in 1987
• Popular language for bioinformatics and web
  programming
• Works well with ASCII text files (flat files)
• Designed to make it easy for one program to
  control other programs
• Supports rapid prototyping
• Portable

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Larry Wall and Perl

• Wall continues to oversee further development of
  Perl and serves as the Benevolent Dictator for
  Life of the Perl project. His role in Perl is
  best conveyed by the so-called 2 Rules, taken
  from the official Perl documentation
• Larry is always by definition right about how
  Perl should behave. This means he has final veto
  power on the core functionality.
• Larry is allowed to change his mind about any
  matter at a later date, regardless of whether he
  previously invoked Rule 1. Got that? Larry is
  always right, even when he was wrong.

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Humor and Perl

• Wall along with Randal L. Schwartz and Tom
  Christiansen writing in the second edition of
  Programming Perl, outlined the Three Virtues of a
  Programmer
• Laziness - The quality that makes you go to great
  effort to reduce overall energy expenditure. It
  makes you write labor-saving programs that other
  people will find useful, and document what you
  wrote so you don't have to answer so many
  questions about it. Hence, the first great virtue
  of a programmer. Also hence, this book. See also
  impatience and hubris.
• Impatience - The anger you feel when the computer
  is being lazy. This makes you write programs that
  don't just react to your needs, but actually
  anticipate them. Or at least pretend to. Hence,
  the second great virtue of a programmer. See also
  laziness and hubris.
• Hubris - Excessive pride, the sort of thing Zeus
  zaps you for. Also the quality that makes you
  write (and maintain) programs that other people
  won't want to say bad things about. Hence, the
  third great virtue of a programmer. See also
  laziness and impatience.

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Getting Perl

• Can be downloaded from www.perl.com
• Version on CSE machines (J251 and 263) is or will
  be on Linux and the vanilla open source version

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Text appendices

• Appendix A Resources
• Appendix B Perl Summary (focusing on what is
  most useful for our purposes in this course)

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Programming

• Edit Run Revise (and Save)
• Program Process
• Identify required inputs
• Design the program, usually an algorithm that
  computes the output from the inputs
• How will output be handled? (display or file)
• Refine the design with more detail
• Write the Perl program code and revise until
  working correctly

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Pseudocode and Code

• getanswer
• sub getanswer
• print Type in your answer here
• my answer
• chomp answer
• return answer

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More pseudocode

• get the name of DNAfile from the user
• read in the DNA from the DNAfile
• for each regulatory element
• if element is in DNA, then
• add one to the count
• print count

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Comments

• Comments are anything on a line after a sign
  until the end of the line (only exception is the
  first line of many Perl programs, something like
  !/usr/bin/perl)

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Assignment

• Read Chapters 1-3 of Perl text and skim
  Appendices A and B at the back of the book
• Check out www.perl.com
• Get ready for Chapter 4