SADR -- Sequence Analysis With Distributed Resources
A WWW-based course

Authors
Christian Büschking and Chris Schleiermacher
Bielefeld University, Germany

Today, molecular biologists often have to analyze genetic data generated in sequencing projects. Many of these tasks can be solved using Internet based tools via the World Wide Web, without having to consider many technical problems like local installation, maintenance and (often) financial aspects. These tools are growing increasingly indispensable for daily sequence analysis work. Still, often questions arise:

Teaching people how to solve these problems using web based sequence analysis with distributed resources, the WWW itself is the medium of choice. Our WWW-based course SADR assumes a minimal background in bioinformatics and so does not explain the algorithms behind the tools. Instead, it emphasizes practical tool usage in connection with the biological considerations that guide the process of sequence analysis.

After presenting a short overview of WWW history, the course gives a general introduction in WWW searchtools and how to find biological resources on the Web.

In the next section, BLAST, we introduce the two main BLAST services at NCBI and GenomeNet. Here, we show which parameters the user has to choose for different scenarios and how to adjust the quantity of optional parameters.

Moreover, we teach how to find sequence information in specific databases, like HIV related sequences or insertion sequences from rhizobia meliloti.

For those who prefer FASTA, we again explain parameter settings for DNA or protein sequence homology searches, and discuss the interpretation of results and the difference to BLAST queries.

Two further lessons deal with pairwise and multiple alignment tools. A lecture about primer generation for the Polymerase chain reaction (PCR) follows.

The next chapter introduces RNA structure and how to fold RNA sequences using mfold, a software tool that predicts secondary structures. Finally, we introduce some publicly available phylogeny tools.

As an ISMB98 tutorial, the course is intended to attract participants that are relatively new to this research community.