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SignalP 4.0: discriminating signal peptides from transmembrane regions
TLDR
SignalP 4.0 was the best signal-peptide predictor for all three organism types but was not in all cases as good as SignalP 3.0 according to cleavage-site sensitivity or signal- peptide correlation when there are no transmembrane proteins present.
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Improved prediction of signal peptides: SignalP 3.0.
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Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
TLDR
A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed and it is estimated that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%.
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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 method…
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Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.
TLDR
An artificial neural network method is presented that predicts phosphorylation sites in independent sequences with a sensitivity in the range from 69 % to 96 % and predicts novel phosphorylated sites in the p300/CBP protein that may regulate interaction with transcription factors and histone acetyltransferase activity.
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Locating proteins in the cell using TargetP, SignalP and related tools
TLDR
The properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts are described and a brief history of methods to predict subcellular localization based on these sorting signals and other sequence properties are sketched.
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A human gut microbial gene catalogue established by metagenomic sequencing
TLDR
The Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals are described, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species.
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Enterotypes of the human gut microbiome
TLDR
Three robust clusters (referred to as enterotypes hereafter) are identified that are not nation or continent specific and confirmed in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous.
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Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence
TLDR
A new method for kinase‐specific prediction of phosphorylation sites, NetPhosK, is presented, which extends the earlier and more general tool, netPhos, and the issues of underestimation, over‐prediction and strategies for improving prediction specificity are discussed.
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Assessing the accuracy of prediction algorithms for classification: an overview
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…
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