Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes

Source Code for Biology and Medicine

Bosco K Ho¹  Andrew J Perry² 

[1] Monash eResearch Centre, Monash University, Melbourne, Australia;Department of Biochemistry, Monash University, Melbourne, Australia

关键词: Bacterial;    Python;    Membrane protein;    Proteomics;    Bioinformatics;   

Others  :  805756
DOI  :  10.1186/1751-0473-8-9

 received in 2012-05-02, accepted in 2013-03-03,  发布年份 2013

【 摘 要 】

Background

The annotation of surface exposed bacterial membrane proteins is an important step in interpretation and validation of proteomic experiments. In particular, proteins detected by cell surface protease shaving experiments can indicate exposed regions of membrane proteins that may contain antigenic determinants or constitute vaccine targets in pathogenic bacteria.

Results

Inmembrane is a tool to predict the membrane proteins with surface-exposed regions of polypeptide in sets of bacterial protein sequences. We have re-implemented a protocol for Gram-positive bacterial proteomes, and developed a new protocol for Gram-negative bacteria, which interface with multiple predictors of subcellular localization and membrane protein topology. Through the use of a modern scripting language, inmembrane provides an accessible code-base and extensible architecture that is amenable to modification for related sequence annotation tasks.

Conclusions

Inmembrane easily integrates predictions from both local binaries and web-based queries to help gain an overview of likely surface exposed protein in a bacterial proteome. The program is hosted on the Github repository http://github.com/boscoh/inmembrane webcite.

【 授权许可】

   
2013 Perry and Ho; licensee BioMed Central Ltd.

【 图 表 】

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