OCTOPUS / SPOCTOPUS – Prediction of Membrane Protein Topology and Signal Peptides

OCTOPUS / SPOCTOPUS

:: DESCRIPTION

OCTOPUS is a new method for predicting transmembrane protein topology is presented and benchmarked using a dataset of 124 sequences with known structures.

SPOCTOPUS is a method for combined prediction of signal peptides and membrane protein topology, suitable for genome-scale studies.

::DEVELOPER

Elofsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

OCTOPUS / SPOCTOPUS

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 1;24(15):1662-8. doi: 10.1093/bioinformatics/btn221. Epub 2008 May 12.
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar.
Viklund H1, Elofsson A.

Bioinformatics. 2008 Dec 15;24(24):2928-9. doi: 10.1093/bioinformatics/btn550. Epub 2008 Oct 22.
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.
Viklund H1, Bernsel A, Skwark M, Elofsson A.

LnSignal – Predicting Protein N-terminal Signal Peptides

LnSignal

:: DESCRIPTION

The web server LnSignal (Labelling N-terminal Signal petide cleavage site) was developed by integrating position-specific amino acid propensities based on the highest average positions and conditional random fields.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Yong-Xian Fan, Jiangning Song, Chen Xu and Hong-Bin Shen,
Predicting protein N-terminal signal peptides using position-specific amino acid propensities and conditional random fields ,
Current Bioinformatics, 2013, 8: 183-192.

Signal-3L 3.0 – A 3-layer Approach for Predicting Signal Peptides

Signal-3L 3.0

:: DESCRIPTION

Signal-3L is an automated method for predicting signal peptide sequences and their cleavage sites in eukaryotic and bacterial protein sequences.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Biochem Biophys Res Commun. 2007 Nov 16;363(2):297-303. Epub 2007 Aug 31.
Signal-3L: A 3-layer approach for predicting signal peptides.
Shen HB1, Chou KC.

Signal-CF – Predicting Signal Peptides

Signal-CF

:: DESCRIPTION

Signal-CF is an automated method for predicting signal peptide sequences and their cleavage sites in eukaryotic and bacterial protein sequences

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Biochem Biophys Res Commun. 2007 Jun 8;357(3):633-40. Epub 2007 Apr 5.
Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides.
Chou KC1, Shen HB.