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Bioinformatics Advance Access originally published online on February 23, 2009
Bioinformatics 2009 25(8):1094-1095; doi:10.1093/bioinformatics/btp100
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PAnnBuilder: an R package for assembling proteomic annotation data

Hong Li 1,2,3, Guohui Ding 1, Lu Xie 2,* and Yixue Li 1,2,*

1Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, 2Shanghai Center for Bioinformation Technology, Shanghai 200235 and 3Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, P.R.China

*To whom correspondence should be addressed.


  Abstract

Summary: PAnnBuilder is an R package to automatically assemble protein annotation information from public resources to provide uniform annotation data for large-scale proteomic studies. Sixteen public databases have been parsed and 54 annotation packages have been constructed based on R environment or SQLite database. These ready-to-use packages cover most frequently needed protein annotation for three model species including human, mouse and rat. Several extended applications such as annotation based on protein sequence similarity are also provided. Sophisticated users can develop their own packages using PAnnBuilder. PAnnBuilder may become an important tool for proteomic research.

Availability: PAnnBuilder and example annotation packages are freely available from http://www.biosino.org/PAnnBuilder/

Contact: xielu{at}scbit.org; yxli{at}sibs.ac.cn

Associate Editor: John Quackenbush

Received on October 26, 2008; revised on January 6, 2009; accepted on February 16, 2009

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