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
Sequence-Based Prediction of Cysteine Reactivity Using Machine Learning
TL;DR: A machine learning method, sbPCR (sequence-based prediction of cysteine reactivity), which combines the basic local alignment search tool, truncated composition of k-spaced amino acid pair analysis, and support vector machine to predict cysteines with hyper-reactivity based on only local sequence features.
Journal ArticleDOI
Aberrant NAD+ metabolism underlies Zika virus–induced microcephaly
Huanhuan Pang,Yisheng Jiang,Jie Li,Yushen Wang,Yushen Wang,Meng Nie,Nan Xiao,Shuo Wang,Zhihong Song,Fansen Ji,Yafei Chang,Yu Zheng,Ke Yao,Li Ang Yao,Shao Li,Peng Li,Peng Li,Lei Song,Xun Lan,Zhiheng Xu,Zeping Hu +20 more
TL;DR: In this paper, a multi-omics study was performed to reveal extensive and large-scale metabolic reprogramming events in ZIKV-infected mouse brains by performing a multisomics study comprising transcriptomics, proteomics, phosphoproteomics and metabolomics approaches.
Journal ArticleDOI
dbPSP: a curated database for protein phosphorylation sites in prokaryotes.
TL;DR: A curated database of phosphorylation sites in prokaryotes for 96 proKaryotic organisms, which belong to 11 phyla in two domains including bacteria and archaea is presented and shows that there were obvious differences among the phosphorylated proteins in bacteria, archaea and eukaryotes.
Journal ArticleDOI
Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast.
Julie Bonne Køhler,Triin Tammsalu,Maria Louise Mønster Jørgensen,Nana Steen,Ronald T. Hay,Geneviève Thon +5 more
TL;DR: Proteome-wide analyses of SUMO modification sites in fission yeast identify over a thousand sumoylated lysines in a total of 468 proteins and quantify changes occurring in theSumO modification status when the STUbL or Ufd1 pathways are compromised by mutations.
Journal ArticleDOI
The Atypical MAP Kinase ErkB Transmits Distinct Chemotactic Signals through a Core Signaling Module.
John M.E. Nichols,John M.E. Nichols,Peggy Paschke,Peggy Paschke,Sew Y. Peak-Chew,Thomas D. Williams,Luke Tweedy,Mark Skehel,Elaine Stephens,Elaine Stephens,Jonathan R. Chubb,Robert R. Kay +11 more
TL;DR: It is shown using phosphoproteomics that different chemoattractants cause phosphorylation of the same core set of around 80 proteins in Dictyostelium cells, which indicates a central role for ErkB and its substrates in directing chemotaxis.
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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