ArticleSource code for biology and medicine2013
Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes.
Article in Source code for biology and medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed, 13 citations in OpenAlex.
- Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species.BMC bioinformatics · 2021Article
- In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB).3 Biotech · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsInmembrane 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.
conclusionsInmembrane 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.
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Registered trials
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