An Introduction to using some web-based sequence handling and analysis tools

This tutorial is designed to introduce you to a range of tools that may help you in the analysis of sequence data throughout the course of your research (The Aims and Objectives of the tutorial can be found here). The tutorial has been divided into four sections.

In the first section we will look at some of the tools available for sequence retrieval and manipulation on the web. We will look at ways of retrieving sequences from the databases and methods for reverse complementing a DNA sequence, restriction analysis, and translating a sequence.

In the second section methods for sequence similarity and database searching will be introduced.

The third section will discuss methods to find conserved motifs within protein sequences.

Finally, in the fourth section you will be briefly introduced to the use of a free web based tool for microarray data handling and analysis.

A few points:

This tutorial requires you to have a basic knowledge of using web browsers, using Word, cutting and pasting, and a working knowledge of molecular biology.

Sometimes the internet can become congested and results may take a while to appear – please be patient.

This tutorial is entirely web based. Simply work through the steps of each exercise recording the results as you go along by copying and pasting into a Word document. You can also copy and past any links to web pages you think might be useful, in a similar fashion. The four different sections can be carried out in any order and although section 1 should really be done first. Varying the order of the sections may help to reduce load on the tools and speed things up.

If you have any problems with the use of any tools or unclear about anything then please feel free to ask one a demonstrator for assistance.

This tutorial is designed to be an introduction to a few useful web based tools. Much more information is available about their use and the way that they work.  There are many more bio-computing tools out there on the Internet. A list of useful links and sites, together with pointers to further reading can be found here.

Please provide feedback on the design of these pages and the way the workshop has been run by filling in this form.

If you have any comments, queries (or you have found any mistakes!) then please contact Neil Wipat.