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:
- How do I detect sequence homologies?
- How do I derive function from possible homologies?
- How do I find references on homologous sequences?
- What is the best tool for reconstructing phylogenies?
- How do I calculate and display the secondary structure of a RNA-molecule?
- Which primers should I use? What is the most transparent tool for
designing them?
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.