Introduction to Bioinformatics Using Action Labs

9781257694891

Introduction to Bioinformatics Using Action Labs

Jean-Louis Lassez

Ryan Rossi

Stephen Sheel

Preface

Bioinformatics is the application of computational techniques and tools to analyze and manage biological data. This book provides an introduction to bioinformatics through the use of Action Labs. These labs allow students to get experience using real data and tools to solve difficult problems. The book comes with supplementary software tools and papers. The labs use data from Breast Cancer, Liver Disease, Diabetes, SARS, HIV, Extinct Organisms, and many others. The book has been written for first or second year computer science, mathematics, and biology students. The supplementary software and papers can be found at http://www.kibazen.com/binf

Jean-Louis Lassez: Life is Pachinko at the Kinsey Institute Museum

Table of Contents

Copyright Page

Title Page

Preface

Chapter 1 - Introduction to Bioinformatics

Chapter 2 - Introduction to BLAST and FASTA

Chapter 3 - BLAST Analysis and Applications

Chapter 4 - Advanced Bioinformatics Tools

Chapter 5 - Classification and Pattern Recognition

Chapter 6 - Advanced Topics

Appendix - Supplementary Papers

Glossary

Index

Chapter 1

Introduction to Bioinformatics

What is Bioinformatics

Background:

What is Bioinformatics? It depends on who you are talking to. A geneticist, a biologist, a mathematician, a CEO of a pharmaceutical company and a computer scientist all would have related, but different, opinions as to what Bioinformatics is.

Purpose:

This lab introduces various aspects of Bioinformatics, its scientific basis, its techniques and its applications.

Resources:

There are many excellent resources on Bioinformatics that can be found on the web. Visit, for instance, the tutorial located at:

http://www.ebi.ac.uk/2can/bioinformatics/bioinf_what_1.html

Key Terms:

Genome

Gene

Protein

Amino Acid

DNA

Codon

Prokaryote

Eukaryote

Archaea

RNA

Directions:

Read the tutorial in the resources (or equivalent) thoroughly.

Exercises:

Give a concise, yet precise, definition of Bioinformatics.

What are the biggest challenges facing Bioinformatics? Why do you think this is the case?

Give a list of the main biological databases that can be accessed on the internet.

What are the differences in the functions of the various biological databases?

Name the categories of the major data analysis tool.

How are the sequence analysis tools used in Bioinformatics?

Make a list of the most important real-world applications for Bioinformatics. Rank your choices from 1-10 and justify why, in your view, the application received its ranking (As the ranking is subjective and tied to your taste or expertise, what matters most is not the ranking you choose but the justifications you give).

References:

European Molecular Biology Laboratory (EMBL).What is Bioinformatics?.

<http://www.ebi.ac.uk/2can/bioinformatics/bioinf_what_1.html>.

Genetic Home Reference: Your Guide to Understanding Genetic Conditions [Internet]. Bethesda, MD: United States National Library of Medicine, National Institute of Health [modified: 2009 July 31]. [Illustration], DNA is a double helix formed by base pairs attached to a sugar-phosphate backbone.;[cited 2007 July][about 3 screens]. Available from:http://ghr.nlm.nih.gov/handbook/basics/dna.

Exploring Frameshifts

Background:

A frameshift mutation (also called a frameshift or a framing error) is a genetic mutation that inserts or deletes a number of nucleotides that are not evenly divisible by three from a DNA sequence. Due to the triplet nature of gene expression by codons, the insertion or deletion disrupts the reading frame, or the grouping of the codons, resulting in a completely different translation from the original. The earlier in the gene the deletion or insertion occurs, the more altered the gene product will become.

Frameshift mutations frequently result in severe genetic diseases.

Purpose:

This lab is intended to analyze how different mutations affect sequences.

Resources:

BLAST: http://www.ebi.ac.uk/blast

Transeq: http://www.ebi.ac.uk/emboss/transeq/

Key Terms:

Frameshift mutation

Codon

Insertion

Deletion

Directions:

Make sure you have an understanding of the keywords above, and then complete the exercises below.

Exercises:

How many ways can we parse this DNA subsequence into a potential coding frame?

………TACGGAAGTTCACTGCAATCAGTTGACTGAGGACTG……

Assume that the coding frame for the subsequence is in fact:

TAC/GGA/AGT/TCA/CTG/CAA/TCA/GTT/GAC/TGA/GGA/CTG

Translate this subsequence into a sequence of amino acids. (You can do it by hand using the table for the genetic code, but using the Transeq program will be easier and faster.)

Now an insertion mutation has happened resulting in the following sequence:

TACGGTAAGTTCACTGCAATCAGTTGACTGAGGACTG

Translate this new sequence into a sequence of amino acids.

Next divide the sequence, which has a deletion mutation, into codons:

TACGAAGTTCACTGCAATCAGTTGACTGAGGACTG

Translate this new sequence into a sequence of amino acids.

Are there significant changes in the translation? Explain the reason for the differences in the translation from questions 3 and 4.

Run the BLAST program on the three DNA sequences above. Do the frameshifts cause a misclassification in the organisms identified by BLAST when compared to the original DNA sequence?

Visit the site: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=442341. Read the abstract for the article. Summarize the authors’ main point.

References:

Schach,B.G., Yoshitake,S. and Davie,E. W., Hemophilia B (factor IXSeattle 2) due to a single nucleotide deletion in the gene for factor IX, The Journal of Clinical Investigation, no. 4(1987),

<http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=442341>.(12 September 2006).

The European Bioinformatics Institute (EBI).Blast @ EBI.<http://www.ebi.ac.uk/blast>.

The European Bioinformatics Institute (EBI). EMBOSS Transeq.<http://www.ebi.ac.uk/emboss/transeq/>.

Genetic Home Reference: Your Guide to Understanding Genetic Conditions [Internet]. Bethesda, MD: United States National Library of Medicine, National Institute of Health [modified: 2009 July 31]. [Illustration], Frameshift mustation.;[cited 2007 July][about 3 screens]. Available from:http://ghr.nlm.nih.gov/handbook/basics/dna.

Bioinformatics Tools

Background:

Molecular Sequence Alignment Tool

Sequence similarity is assessed, in a first instance, by comparing the first, and then second, then third, etc. letters from each sequence and scoring positive points when there is a match and negative points when there is no match. The problem becomes more complex when we have gaps, which occur when one sequence may have been subjected to one or more insertion or deletion mutations. This lab provides an introduction to sequence alignment, which is the first fundamental tool in the study of biosequences.

Here is an example of alignment:

410 AANCGTGATCGATGCTAGCTATATA 434

410 AATCGTTATCGATGCTAGCTATATA 434

The numbers at each end of the sequences correspond to the nucleotide number in the original sequence. The (|) means a match, while (:) means a gap and no connector means a substitution, as we see on the seventh pair.

Purpose:

This lab introduces Molecular Sequence Alignment tools.

Resources:

For this exercise use the software located at:

http://xylian.igh.cnrs.fr/bin/align-guess.cgi.

Key Terms:

Genome

Sequence Alignment

Mutation

Insertion/deletion/substitution

Gap Penalty

E-score

Nucleotide

Directions:

As will often happen with online bioinformatics resources, links, such as the one in the resources may or may not work. It is part of this lab to train you in searching the net until you find the appropriate information. Once you are at the website, or another equivalent one, run the alignment tool with the sequences below.

First Sequence:

AACGCCCAGGGTTTCCCAGTCACGACGTTGTAAAAGCGACGGCCAGTGCCA

Second Sequence:

AACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGCCA

Exercises:

What percentage identity do these two sequences have?

What is the gap penalty and where is/are the gap(s) in the alignment?

What is the score of the alignment?

The next exercises make use of an ORF finder and the sequence below.

The link to ORF Finder is: http://www.ncbi.nlm.nih.gov/gorf/gorf.html

Give the following sequence as input to the program:

4. What do the colored bars represent in the frames?

5. Which frame does not contain an open reading frame?

6. Which frame has the longest open reading frame?

7. Which of these ORF’s, if any, correspond to a known gene?

References:

Institut de Génétique Humaine. ALIGN Query using sequence data. <http://xylian.igh.cnrs.fr/bin/align-guess.cgi>.

National Center for Biotechnology Information (NCBI). ORF Finder (Open Reading Frame Finder).

<http://www.ncbi.nlm.nih.gov/gorf/gorf.html>.

Chapter 2

Introduction to BLAST and FASTA

Introduction to Sequence Analysis

Database Searching Options

Statistical matrices allow a query sequence to be aligned with matching sequences in the database. The less complex, faster matrices sacrifice a certain degree of match significance. The matrix together with the choice of the program essentially determines the search sensitivity and speed.

Filtering masks regions of the query sequence that has repeats or other low compositional complexity areas. Masking is achieved by replacing the repeats with N’s, the IUB code for any base.

The three main public molecular databases are EMBL(Europe), GenBank(US), and DDBJ(Japan). These three databases update each other with new sequences collected from each region, every 24 hours.

Every entry into the database requires a unique identifier that never changes and a version number.

A redundant database is a database where more than one copy of each variant of a sequence may be found. The advantage of a redundant database is that it’s much more likely to contain recently discovered sequences. The disadvantage is that the biologically significant results are more likely to be hidden among the large number of reported matches.

Sequence Alignment Programs

BLAST – BLAST is the fastest, but compromises some degree of sensitivity for speed.

FASTA – FASTA is slower, but more sensitive then BLAST.

BLITZ – BLITZ also provides a very sensitive search but is very slow to run.

BLAST and FASTA