Journal ArticleDOI
pLogo: a probabilistic approach to visualizing sequence motifs
TLDR
The pLogo is described, a motif visualization in which residue heights are scaled relative to their statistical significance, in which real-time conditional probability calculations and visualizations are supported.Abstract:
Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at http://plogo.uconn.edu/ and supports real-time conditional probability calculations and visualizations.read more
Citations
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Journal ArticleDOI
Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.
TL;DR: An isotope-tagged cleavable linker (isoTCL) strategy was developed, which enabled isotopic labeling of O-GlcNAc through bioorthogonal conjugation of affinity tags and demonstrated the application of the isoTCL in mapping and quantification ofO-GlCNAcylation sites in HeLa cells.
Journal ArticleDOI
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.
Jiawei Wang,Bingjiao Yang,Yi An,Tatiana T. Marquez-Lago,André Leier,Jonathan J. Wilksch,Qingyang Hong,Yang Zhang,Morihiro Hayashida,Tatsuya Akutsu,Geoffrey I. Webb,Richard A. Strugnell,Jiangning Song,Trevor Lithgow +13 more
TL;DR: A state-of-the-art T4SE predictor is developed by conducting a comprehensive performance evaluation of different machine learning algorithms along with a detailed analysis of single- and multi-feature selections.
Journal ArticleDOI
Systematic and Quantitative Assessment of Hydrogen Peroxide Reactivity With Cysteines Across Human Proteomes.
Ling Fu,Keke Liu,Ming-an Sun,Caiping Tian,Rui Sun,Rui Sun,Carlos Morales Betanzos,Keri A. Tallman,Ned A. Porter,Yong Yang,Dianjing Guo,Daniel C. Liebler,Jing Yang +12 more
TL;DR: A chemoproteomic platform to systematically and quantitatively analyze the reactivity of thousands of cysteines toward H2O2 in human cells is described and provides an opportunity to predict oxidation-triggered protein conformational changes.
Journal ArticleDOI
iDNA6mA-Rice: A Computational Tool for Detecting N6-Methyladenine Sites in Rice.
TL;DR: A machine learning-based method of predicting 6mA sites in the rice genome using mono-nucleotide binary encoding and Random Forest to perform the classification and an area under the receiver operating characteristic curve of 0.981 was obtained, suggesting that the proposed method had good performance.
Journal ArticleDOI
GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins.
TL;DR: This work compiled a benchmark data set containing 3098 known S-palmitoylation sites identified from small- or large-scale experiments, and developed a new method named DQD to distinguish data quality weights (DQWs) between the two types of the sites, and designed a new predictor called GPS-Palm.
References
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Journal ArticleDOI
WebLogo: A Sequence Logo Generator
TL;DR: WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment that provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive.
Journal ArticleDOI
Sequence logos: a new way to display consensus sequences
Thomas D. Schneider,R M Stephens +1 more
TL;DR: From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content at every position in a site or sequence.
Journal ArticleDOI
A C-terminal signal prevents secretion of luminal ER proteins
Sean Munro,Hugh R.B. Pelham +1 more
TL;DR: It is proposed that the KDEL sequence marks proteins that are to be retained in the ER and discuss possible retention mechanisms.
Journal ArticleDOI
The P-loop--a common motif in ATP- and GTP-binding proteins.
TL;DR: Current knowledge of P-loops is discussed with the additional aim of illustrating the fascinating relationship between protein sequence, structure and function.
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