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SignalP 4.0: discriminating signal peptides from transmembrane regions
We benchmarked SignalP 4.0 against SignalP 3.0 and ten other signal peptide prediction algorithms (Fig. 1). We compared prediction performance using the Matthews correlation coefficient16, for whichExpand
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Improved prediction of signal peptides: SignalP 3.0.
We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hiddenExpand
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Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed. Using N-terminal sequence information only, it discriminatesExpand
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Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
We have developed a new method for the identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence. The methodExpand
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Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.
Protein phosphorylation at serine, threonine or tyrosine residues affects a multitude of cellular signaling processes. How is specificity in substrate recognition and phosphorylation by proteinExpand
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Locating proteins in the cell using TargetP, SignalP and related tools
Determining the subcellular localization of a protein is an important first step toward understanding its function. Here, we describe the properties of three well-known N-terminal sequence motifsExpand
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A human gut microbial gene catalogue established by metagenomic sequencing
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly andExpand
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Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence
Post‐translational modifications (PTMs) occur on almost all proteins analyzed to date. The function of a modified protein is often strongly affected by these modifications and therefore increasedExpand
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Assessing the accuracy of prediction algorithms for classification: an overview
TLDR
We provide a unified overview of methods that currently are widely used to assess the accuracy of prediction algorithms, from raw percentages, quadratic error measures and other distances, and correlation coefficients, to information theoretic measures such as relative entropy and mutual information. Expand
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Enterotypes of the human gut microbiome
Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world.Expand
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