WebLogo: a sequence logo generator.

By Gavin E. Crooks, Gary Chung Hon, John-Marc Chandonia, Steven E. Brenner. 2004

12,372 citations recorded by the source corpus.

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos 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. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization.

Subfields: Molecular Biology

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Citations in the corpus

ProGen: Language Modeling for Protein Generation (2020, background): “The sequence logo [13] between a wild hen lysozyme multiple sequence alignment (MSA) resembles the sequence logo of a ProGen-generated lysozyme library.”
Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein (2013, methodology): “Logo plots from these sequences were created using WebLogo 3.0 (Crooks et al. 2004).”
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks (2005, methodology): “This procedure allowed us to reject a small number of false positive sites identified after scanning of microbial genomes (Table 3). Sequence logos for derived regulatory motifs were drawn using WebLogo package v.2.6 [ 64 ] (http://weblogo.berkeley.edu/).”
bpRNA: large-scale automated annotation and analysis of RNA secondary structure (2018, background): “Sequence logos (48) for all tetraloop tokens and for the top 1% when sorted by type frequency is presented in Figure 4B.”
Genomic Organization, Differential Expression, and Interaction of SQUAMOSA Promoter-Binding-Like Transcription Factors and microRNA156 in Rice1[W] (2006, methodology): “The HMM profile of the SBP domain was reconstructed with the HMMbuild program in the HMMER package version 2.1 (Eddy, 1998), and alignment was viewed with sequence LOGO (Crooks et al., 2004).”
Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system (2006, background): “, which provides a visual display of the information content and frequency of each base at each position within the motif (a web-based Sequence logo generato”
Minimal tool set for a prokaryotic circadian clock (2016, methodology): “Afterwards the alignments were adjusted to Synechococcus 7942 sequence with Jalview [85] and edited multialignments were used to create WebLogos [86].”
Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences (2017, neutral): “We trained models that simply used k-mer counts in each 5 ′ UTR as features as well as training models using k-mers at each position as features (e.g., for a 3-mer model, there are 64 possible 3-mer sequences and 48 positions, leading to 3072 model weights; 3072 = 43 × 48).”
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution (2010, methodology): “The graphic representation was generated using Weblogo 3 (ref”
The C. elegans TGF-β Dauer Pathway Regulates Longevity via Insulin Signaling (2007, positive): “p values for BioProspector motifs were generated by the performance of 35 Monte Carlo simulations so that the null motif score distribution could be estimated [12]; Weeder’s p value calculator was used for motif significance. Motifs were displayed in WebLogo [ 30 ].”