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
Logomaker: beautiful sequence logos in Python.
Ammar Tareen,Justin B. Kinney +1 more
TL;DR: Logomaker is a Python API for creating publication-quality sequence logos that can produce both standard and highly customized logos from either a matrix-like array of numbers or a multiple-sequence alignment.
Journal ArticleDOI
Molecular recordings by directed CRISPR spacer acquisition
Seth L. Shipman,Seth L. Shipman,Jeff Nivala,Jeff Nivala,Jeffrey D. Macklis,George M. Church,George M. Church +6 more
TL;DR: A recording system that uses the nucleotide content, temporal ordering, and orientation of defined DNA sequences within a CRISPR array in order to encode arbitrary information within the genomes of a population of cells is established.
Journal ArticleDOI
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites
Jiangning Song,Yanan Wang,Fuyi Li,Tatsuya Akutsu,Neil D. Rawlings,Geoffrey I. Webb,Kuo-Chen Chou +6 more
TL;DR: iProt-Sub will be a powerful tool for proteome-wide prediction of protease-specific substrates and their cleavage sites, and will facilitate hypothesis-driven functional interrogation of prote enzyme-specific substrate cleavage and proteolytic events.
Journal ArticleDOI
Proteome-Wide Identification of SUMO2 Modification Sites
TL;DR: A novel method that enabled proteome-wide identification of sumoylated lysines that involves the expression of polyhistidine–tagged SUMO2 with Thr90 mutated to Lys and developed a method to discover the exact sites to which SUMOs conjugate.
Journal ArticleDOI
A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging
Haopeng Xiao,Mark P. Jedrychowski,Devin K. Schweppe,Edward L. Huttlin,Qing Yu,David E. Heppner,Jiaming Li,Jiani Long,Evanna L. Mills,John Szpyt,Zhixiang He,Guangyan Du,Ryan Garrity,Anita Reddy,Laura Pontano Vaites,Joao A. Paulo,Tinghu Zhang,Nathanael S. Gray,Steven P. Gygi,Edward T. Chouchani +19 more
TL;DR: Oximouse is developed, a comprehensive and quantitative mapping of the mouse cysteine redox proteome in vivo that comprehensively identifies redox-modified disease networks that remodel in aged mice, establishing a systemic molecular basis for the long-standing proposed links between redox dysregulation and tissue aging.
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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