Building a Multiuser Sequence Analysis Facility Using Freeware
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Although many commercial packages exist for molecular sequence analysis, they are typically expensive. Whereas many Web-based applications are available for sequence analysis, the Web interface cannot store data on remote servers and is awkward to use. A good alternative is to build a sequence analysis facility on a local server. BIRCH, the Biological Research Computer Hierarchy, is an example of such a system (http://home.cc.umanitoba.ca/~psgendb and ref. 1). BIRCH is best thought of as a workbench containing tools for working with sequences, as well as software that minimizes the problems of putting tools together to perform a task. For example, in Fig. 1 , several steps in phylogeny construction from an alignment were performed automatically. It is not possible to provide detailed instructions on installing all of the 300+programs that currently reside in BIRCH. Rather, my purpose is to outline the strategies and tricks that make building and maintaining a sequence facility a smooth ongoing task.
Fig. 1. Automated phylogeny. In GDE ( 2 ), aligned sequences were selected, and fastDNAml ( 3 ) was called to produce a phylogeny. GDE automatically calls a text editor and treetool ( 4 ) to display results.
