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Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(3) © Oxford University Press 2004; all rights reserved.

Applications Note

HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data

Susanna Lamers 1, Scott Beason 1, Luke Dunlap 1, Robert Compton 1 and Marco Salemi 2,*

1 Gene Johnson Inc., St Augustine, FL, USA and 2 Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA, USA

Received on August 20, 2003 ; accepted on September 17, 2003
Advance Access Publication January 22, 2004

Background: Human immunodeficiency virus (HIV) research involves ongoing, repetitious sequencing of the HIV genome and the massive accumulation of associated investigational data. As a result, the storage of annotated DNA and/or protein sequences, as well as information retrieval, have become increasingly difficult tasks, with scientists extracting less information from their collected data than they should.

Objectives: Our objective was to design and develop a software package to aid researchers in the storage, analysis and exploration of their HIV-associated data.

Results: HIVbase contains familiar, easy-to-use interfaces and functionality for integrating many types of disparate data. The software contains tools that allow for the mass import of raw genetic data, eliminate repetitious sequence translations, have the ability to identify automatically and store HIV regions of interest from nucleic acid or protein sequences, allow for the export of data in commonly used analysis-ready formats, and for unique querying approaches.

Contact: msalemi68{at}hotmail.com

* To whom correspondence should be addressed.


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