Abstract
| Original language | English |
|---|---|
| Article number | 9 |
| Pages (from-to) | 1 - 9 |
| Number of pages | 9 |
| Journal | Source Code for Biology and Medicine |
| Volume | 8 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - 2013 |
Cite this
}
Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes. / Perry, Andrew James; Ho, Bosco Kwan-Chung.
In: Source Code for Biology and Medicine, Vol. 8, No. 1, 9, 2013, p. 1 - 9.Research output: Contribution to journal › Article › Research › peer-review
TY - JOUR
T1 - Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes
AU - Perry, Andrew James
AU - Ho, Bosco Kwan-Chung
PY - 2013
Y1 - 2013
N2 - 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.
AB - 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.
UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668253/pdf/1751-0473-8-9.pdf
U2 - 10.1186/1751-0473-8-9
DO - 10.1186/1751-0473-8-9
M3 - Article
VL - 8
SP - 1
EP - 9
JO - Source Code for Biology and Medicine
JF - Source Code for Biology and Medicine
SN - 1751-0473
IS - 1
M1 - 9
ER -