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
Changes in metabolic landscapes shape divergent but distinct mutational signatures and cytotoxic consequences of redox stress.
Natalya Degtyareva,Victoria C. Placentra,Scott A. Gabel,Leszek J. Klimczak,Dmitry A. Gordenin,Brett A. Wagner,Garry R. Buettner,Geoffrey A. Mueller,Tatyana I. Smirnova,Paul W. Doetsch +9 more
TL;DR: In this paper , NMR-based analysis of molecular outcomes of redox stress revealed profound dissimilarities in metabolic landscapes following exposure to hydrogen peroxide versus potassium bromate.
Posted ContentDOI
Linear motif specificity in signaling through p38α and ERK2 mitogen-activated protein kinases
TL;DR:
Journal ArticleDOI
XGB5hmC: Identifier based on XGB model for RNA 5-hydroxymethylcytosine detection
Hilal Tayara,Kil To Chong +1 more
TL;DR: XGB5hmC as mentioned in this paper is a high-performance identifier of RNA 5-hydroxymethylcytosine (5-hmC) sites using gradient boosting.
Posted ContentDOI
A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes
Brett W. Engelmann,Chiaowen Joyce Hsiao,John D. Blischak,Yannick Fourne,Michael J. Ford,Yoav Gilad +5 more
TL;DR: In this paper, the authors quantified protein phosphorylation levels for three genotyped human cell lines within a nested experimental framework, and found that genetic background is the primary determinant of protein phosphoproteome variation.
DissertationDOI
Protein adducts and crosslinking by reactive metabolites of polychlorinated biphenyls (PCBs)
TL;DR: In this article, a method to measure PCB adducts with cysteine residues of proteins and to identify the reactive intermediates involved in adduct formation: quinones or arene oxides, or both.
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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