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Bioinformatics Advance Access first published online on May 5, 2007
This version published online on May 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm120
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BioDownloader: Bioinformatics downloads and updates in a few clicks

Maxim V. Shapovalov , Adrian A. Canutescu and Roland L. Dunbrack, Jr. *

Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia PA 19111 USA

*To whom correspondence should be addressed. Dr. Roland Dunbrack, E-mail: Roland.Dunbrack{at}fccc.edu


  Abstract

Summary: There are many ftp or http servers storing data required for biological research. While some download applications are available, there is no user-friendly download application with a graphical interface specifically designed and adapted to meet the requirements of bioinformatics. BioDownloader is a program for downloading and updating files from ftp and http servers. It is optimized to work robustly with large numbers of files. It allows the selective retrieval of only the required files (batch downloads, multiple file masks, ls-lR file parsing, recursive search, recent updates, etc). BioDownloader has a built-in repository containing the settings for common bioinformatics file-synchronization needs, including the PDB and NCBI databases. It can post-process downloaded files, including archive extraction and file conversions.

Availability: The program can be installed from http://dunbrack.fccc.edu/BioDownloader. The software is freely available for both non-commercial and commercial users under the BSD license.

Associate Editor: Prof. Alfonso Valencia

Received on January 6, 2007; revised on March 17, 2007; accepted on March 17, 2007

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