Improved visualization of protein consensus sequences by iceLogo

By Niklaas Colaert, Kenny Helsens, Lennart Martens, J. Vandekerckhove, Kris Gevaert. Nature Methods, 2009

721 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/62068bc615700df56154661fcc180b1fefa7cf15

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In Molecular Biology

Citations in the corpus

Cleavage Entropy as Quantitative Measure of Protease Specificity (2013, methodology): “consensus recognition motives and visualization by sequence logos [34], iceLogo [35] or heat maps [29].”
Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion (2012, background): “Moreover, to the best of our knowledge, all public sequence logo servers, with the exception of the Icelogo (4) and two-sample logo (5) methods, focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion.”
SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks (2013, positive): “924 Cell Metabolism 18, 920–933, December 3, 2013 ª2013 Elsevier Inc. the amino acid sequences surrounding all succinylated sites to nonsuccinylated sites (Figure 3C) or all SIRT5 target sites to nontarget succinylated sites (Figure 3D) by IceLogo (https:// code.google.com/p/icelogo/).”
Log-odds sequence logos (2015, neutral): “A variety of alternative methods for calculating and presenting logos have since been described (Colaert et al., 2009; O’Shea et al., 2013; Schuster-B€ ockler et al., 2004; Vacic et al., 2006; Workman et al., 2005). A logo is derived from a multiple alignment, and represents each position of the ali”
Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation. (2013, methodology): “Filled logo motifs were generated using iceLogo (Colaert et al., 2009).”
A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles (2011, methodology): “To examine the properties of amino acids surrounding ubiquitylation sites, the frequencies of neighboring amino acid residues were compared for ubiquitylated lysines and nonubiquitylated lysines on ubiquitylated proteins using iceLogo (40).”
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. (2013, methodology): “acetyl sites quantified in the study using iceLogo (Colaert et al., 2009).”