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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Posted ContentDOI
Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime
Zeenat B. Noordally,Zeenat B. Noordally,Matthew Hindle,Sarah F. Martin,Daniel D Seaton,Thomas Simpson,Thierry Le Bihan,Andrew J. Millar +7 more
TL;DR: In this article, the authors compare transcriptome data under light-dark cycles (LD) to the algal proteome and phosphoproteome, assayed using shotgun mass-spectrometry.
Journal ArticleDOI
Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction
TL;DR: Hyb4mC as discussed by the authors adopts the DNA2vec method for sequence embedding, which captures more efficient and comprehensive information compared with the sequence-based feature method, and combines the attention mechanism with a text convolutional neural network for further feature learning.
Journal ArticleDOI
Ozone-derived oxysterols impair lung macrophage phagocytosis via adduction of some phagocytosis receptors.
TL;DR: A novel mechanism for the suppression of macrophage phagocytosis following ozone exposure is suggested through the generation of oxysterols and the formation of Oxysterol-protein adducts onPhagocytic receptors.
Journal ArticleDOI
Phosphotyrosine Substrate Sequence Motifs for Dual Specificity Phosphatases.
Bryan M. Zhao,Sarah L. Keasey,Joseph E. Tropea,George T. Lountos,Beverly Dyas,Scott Cherry,Sreejith Raran-Kurussi,David S. Waugh,Robert G. Ulrich +8 more
TL;DR: Analysis of peptide dephosphorylation by hierarchical clustering indicated that DUSPs could be organized by substrate sequence motifs, and peptide-specificities by phylogenetic relationships among the catalytic domains.
Posted ContentDOI
Deep mutational analysis reveals functional trade-offs in the sequences of EGFR autophosphorylation sites
TL;DR: The results show how EGFR-family phosphosites achieve a trade-off between minimizing off-pathway phosphorylation while maintaining the ability to recruit the diverse complement of effectors required for downstream pathway activation.
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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