Applied Bioinformatics for Biologists

A two-day course

October 27 and 28, 2003

Instructors: Fran Lewitter,Ph.D., Head of Biocomputing; George Bell, Ph.D., Bioinformatics Scientist; Robert Latek, Ph.D., Senior Bioinformatics Scientist, Bingbing Yuan, Ph.D., Biocomputing Applications Programmer.

Purpose: This two-day, intensive course will introduce you to the broad scope of bioinformatics, discuss the theory and practice of computational methods, and demonstrate the basic programming tools used in the field of genomics.

Format: A bioinformatics server will be available to class participants for a two-month period so students can do homework problems and practice the tools taught in class.

Who Should Take this Class?
This course is appropriate for lab biologists or lab managers with a good understanding of molecular biology. Familiarity with web-based bioinformatics tools is a plus, but not a requirement.

Course Objectives
From this course, you will: Course Material
There is no book required for this course, but the following are recommended:
Syllabus: Homework Course Evaluation Form
9-10:30 Sequence Analysis I. Pairwise alignments, database searching, BLAST, BLAT and more Dr. Fran Lewitter, Head of Biocomputing, Whitehead Institute This segment will discuss how to effectively do database searches and explore the many parameters to consider when doing a database search. Why do alignments? How are they scored? What methods are available for alignments and database searching? To print, Slide show
10:30-11 Break
11-11:30 Sequence Analysis II. Pattern searching Dr. Fran Lewitter, Head of Biocomputing, Whitehead Institute Pattern searching can be very useful to explore sequence data. Rather than searching data with a sequence, you can search using patterns that might identify important motifs in your data. Class Demo, To print, Slide show
11:30-12:30 Sequence Analysis III. Gene finding methods Dr. Fran Lewitter, Head of Biocomputing, Whitehead Institute We will explore Hidden Markov models (HMMs) and other methods to identify genes in genomic sequence. To print, Slide show
12:30-1:30 Lunch
1:30-2:30 Computational Methods I. Genomic Resources and Unix. Dr. George Bell, Bioinformatics Scientist, Whitehead Institute This topic includes a review of genome browsers that are integrative resources supporting the genome project. You will learn where to download the latest genome data for your organism of study and how to use UNIX to make use of these data resources.   To print, Slide show
2:30-3:00 Break
3:00-4:00 Computational Methods II. Sequence analysis with Perl Dr. George Bell, Bioinformatics Scientist, Whitehead Institute You will learn the basics of programming with Perl, a scripting language used extensively in bioinformatics. Examples of basic scripts will be presented.   To print, Slide show
4:00-5:00 Computational Methods III. Sequence analysis with Perl: modules and BioPerl Dr. George Bell, Bioinformatics Scientist, Whitehead Institute This session will continue the discussion of Perl and will demonstrate how to write web scripts, draw graphics and use BioPerl.   To print, Slide show
9-10:15 Comparative Protein Analysis I. Phylogenetic Trees and Multiple Sequence Alignments Dr. Robert Latek, Senior Bioinformatics Scientist, Whitehead Institute Being able to make comparisons across a series of sequences is an integral part of understanding how they are related. We will explore evolutionary similarities and differences among sets of sequences using phylogenetic trees and multiple sequence alignments to illustrate local and global sequence/function conservation.To print, Slide show
10:15-10:45 Break
10:45-11:30 Comparative Protein Analysis II. Sequence Pattern and Profile Database Searching Dr. Robert Latek, Senior Bioinformatics Scientist, Whitehead Institute Evolution has shuffled a limited number of basic building blocks (domains) to give rise to a diverse repertoire of proteins. We will examine methods to extract these conserved modules and use them to data mine database resources in order to find related proteins and to predict their functions. To print, Slide show
11:30-12:30 Comparative Protein Analysis III. Protein Structure Prediction and Comparison Dr. Robert Latek, Senior Bioinformatics Scientist, Whitehead Institute Protein structures and models are valuable tools in determining protein function, predicting effects of point mutations, finding potential ligands, and construct design. We will investigate several techniques to predict protein structural features and use this information to perform structural comparisons. Structure visualization and annotation will be key components of this process.To print, Slide show
12:30-2:00 Lunch
2:00-3:30 Functional Genomics. Microarray Data Analysis Dr. Fran Lewitter, Head of Biocomputing, Whitehead Institute Normalization techniques: Many sources of systemic variation can arise in microarray experiments that affect the measured gene expression levels. We will discuss methods to remove this type of variation prior to analyzing data. Clustering methods: We will review the underlying assumptions of common clustering methods used to find genes with common expression patterns.   To print, Slide show
3:30-4:00 Break
4:00-4:45 Research Talk: "Using Computational Biology to Understand Human Disease" Mark Daly, Whitehead/Pfizer Computational Biology Fellow
4:45-5:30 Demo: How to use these tools on the Bioinformatics server Here we will provide instructions for you to use our bioinformatics server (through the end of 2003) to perform the type of analyses covered in this course. Access to this server will permit you to do the homework problems accompanying each section of the course.