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Building a Multiuser Sequence Analysis Facility Using Freeware

  • Protocol
Bioinformatics Methods and Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 132))

Abstract

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.

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.

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References

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Authors
  1. Brian Fristensky
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Editor information

Editors and Affiliations

  1. Queen’s University, Kingston, Ontario, Canada

    Stephen Misener

  2. Wayne State University, Detroit, MI

    Stephen A. Krawetz

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© 2000 Humana Press Inc., Totowa, NJ

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Fristensky, B. (2000). Building a Multiuser Sequence Analysis Facility Using Freeware. In: Misener, S., Krawetz, S.A. (eds) Bioinformatics Methods and Protocols. Methods in Molecular Biology™, vol 132. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-192-2:131

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  • DOI: https://doi.org/10.1385/1-59259-192-2:131

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-0-89603-732-8

  • Online ISBN: 978-1-59259-192-3

  • eBook Packages: Springer Protocols

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