Introduction to Bioinformatics: Alignment and database searches

Transparencies

My Powerpoint presentation has been made available as both the Powerpoint presentation it self and a set of web pages. You might want to follow the presentation on your own screen.

• Powerpoint version
• Web page version

Links to web-based tools

• DOTLET - an applet for making dotplots
• LALIGN - a tool for performing local (Smith-Waterman) alignment
• SIM - alternative local alignment tool
• FASTA - fast database search tool
• BLAST - faster database search tool
• PSI-BLAST - iterative BLAST using profiles
• CD-BLAST - Fast search of sequence against profile database
• Genestream - a web server with many different alignment methods

Exercises

There will be short exercises during the lecture. These are:

• Exercise 1
• Exercise 2
• Exercise 3
• Exercise 4

• Pairwise alignment
• Database searching

Links to online tutorials

You are not required to read any of the material below. But if you are looking for more information on sequence alignment these are definately good places to start:

• Online Lectures on Bioinformatics at the German Cancer Research Center
• Pairwise Sequence Alignment at University of Bielefeld
• A Gentle Guide to Multiple Alignment also at University of Bielefeld