A motif visualization in which residue heights are scaled relative to their statistical significance. It supports real-time conditional probability calculations and visualizations.
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Builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol. The unique advantages of iceLogo compared to other sequence logo creating tools is that iceLogo has a more dynamic nature and is more correct and complete in the analysis of conserved sequence patterns.
A web based application designed to make the generation of sequence logos easy and painless.
A web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences.
Integrates detection and visualization of position-specific ultra-short motifs within macromolecules. kpLogo overcomes the limitations of conventional motif-visualization tools in handling positional interdependencies and utilizing ranked or weighted sequences increasingly available from high-throughput assays. It generates a new type of logo plot called the k-mer logo, in which at each position the most significant k-mer is plotted vertically with the total height scaled to its P value or test statistics, as appropriate. kpLogo can be accessed at a simple webserver which generates frequency, information-content, and probability logos in addition to k-mer logos. Its source code is freely available.
A Web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. The source code is distributed under the MIT Open Source license agreement and is available for download free of charge.
Infers the genetic code directly from a newly sequenced, unannotated genome.
Generates publication-quality sequence logos. ggseqlogo employs a method based on the use of polygons to draw elongated letters in ggplot2. It provides numerous features that allow tweaking of the sequence logo. The tool offers high degree of flexibility and customisability through integration with ggplot2. It allows elements such as rectangles, lines, arrows and text to be precisely overlaid onto the logo, programmatically.
A Web based application designed to make the generation of sequence logos from biological sequence alignments simple.
Helps visualize the conservation and entropy of orthologous DNA and protein sequences by presenting them as one long sequence logo that can be zoomed in and out of, from an overview of the entire sequence down to just a few residues at a time. A search function enables users to find motifs such as cis-elements in promoter regions by simply ‘drawing’ a sequence logo representation of the desired motif as a query. Gene Slider combines the ability to make long sequence logos with a search panel that automatically highlights motifs of interest, even when there is a high degree of wobble.
A tool for creating logos representing both sequence alignments and profile hidden Markov models.
Allows users to produce generalized string-based logo. Logolas provides a method to highlight both enrichment and depletion of elements at each position in a sequence. It offers several features such as: the ability to use strings instead of characters; various customizable styles and color palettes; several methods for scaling stack heights; and ease of integrating logo plots with external graphics like ggplot.
Generates DNA sequence logos. DNAlogo can read matrices designating the bit values of each character directly. It can create both bit logos and frequency logos. Frequency logos contain only the information of frequencies of the four nucleotides, but no information of sequence conservation. DNAlogo minimizes the bias introduced by different GC contents. It creates DNA sequence logos with simple operation, and no programming knowledge needed.
Sequence logos for DNA sequence alignments. seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo.
Uses amino acid sequence alignment to generate sequences logos. SeqLogos allows visualization of sequence patterns and represents an informative alternative to consensus sequence.
Permits to represent multiple motifs with different similarity scores. motifStack is able to draw amino acid sequence as easy as to draw DNA/RNA sequence. It allows users to select the font type and symbol colors. The tool calculates mean of multiple motifs position to merge them.
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A web-based tool that generates sequence logos from various input sources.
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Enables to observe the intra-motif dependencies and to visualize the position-specific nucleotide diversity or consensus. CircularLogo allows users to create sequence logo for revealing pairwise dependencies among residues within a motif. It offers the panorama of DNA or RNA motifs taking into consideration the intra-site dependencies. This tool can depict complex dependencies within motifs and reveal biomolecular structure (such as stem structures in tRNA).
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Analysis of P Loop and its Flanking Region Subsequence of Diverse NTPases Reveals Evolutionary Selected Residues
Tools (4):
Jalview, Clustal W, MEGA, WebLogo
Topics (2):
WGS analysis, De novo sequencing analysis
Conserved presence of G quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses
Tools (5):
USEARCH, WebLogo, PhysBinder, Clustal W, MEGA
Topics (4):
De novo sequencing analysis, Homo sapiens, Human immunodeficiency virus 1, Bos taurus
Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA–microRNA regulatory network in nasopharyngeal carcinoma model systems☆
Tools (3):
VarScan, ANNOVAR, WebLogo
Topics (6):
WGS analysis, Homo sapiens, Neoplasms, Glandular and Epithelial, Neoplasms, Epstein-Barr Virus Infections, Herpesviridae Infections
Growth Phase Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein
Tools (3):
Clustal Omega, SMS, WebLogo
Topics (2):
WGS analysis, Halobacterium salinarum
Patterns of genomic variation in the poplar rust fungus Melampsora larici populina identify pathogenesis related factors
Tools (3):
BLASTP, Clustal W, WebLogo
Topics (7):
WGS analysis, De novo sequencing analysis, Melampsora larici-populina, Disease, Hemorrhagic Fevers, Viral, Flaviviridae Infections, Tick-Borne Diseases
The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
Tools (3):
BioProspector, WebLogo, PREDetector
Topics (3):
De novo sequencing analysis, Genome annotation, Escherichia coli
Human Tetherin Exerts Strong Selection Pressure on the HIV 1 Group N Vpu Protein
Tools (3):
MultAlin, WebLogo, Clustal W
Topics (9):
WGS analysis, De novo sequencing analysis, Genome annotation, Human immunodeficiency virus 1, Homo sapiens, Pan troglodytes, Sexually Transmitted Diseases, Viral, Retroviridae Infections, HIV Infections
The driving force of prophages and CRISPR Cas system in the evolution of Cronobacter sakazakii
Tools (6):
SPAdes, Prokka, GET_HOMOLOGUES, PHASTER, CRISPRFinder, WebLogo
Topics (3):
De novo sequencing analysis, Cronobacter sakazakii, Homo sapiens
Selection Driven Extinction Dynamics for Group II Introns in Enterobacteriales
Tools (3):
WebLogo, MAFFT, MEGA
Topics (1):
De novo sequencing analysis
Abundant Oligonucleotides Common to Most Bacteria
Tools (3):
Clustal W, Jalview, WebLogo
Topics (4):
WGS analysis, De novo sequencing analysis, Genome annotation, Heterocyclic Compounds, 2-Ring
The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales
Tools (6):
BLASTN, BLASTX, CLC Main Workbench, Clustal W, WebLogo, MEGA
Topics (3):
WGS analysis, De novo sequencing analysis, Chalcogens
Genetic Analysis of Loop Sequences in the Let 7 Gene Family Reveal a Relationship between Loop Evolution and Multiple IsomiRs
Tools (3):
MEGA, SplitsTree, WebLogo
Topics (7):
Protein sequence analysis, WGS analysis, De novo sequencing analysis, RNA-seq analysis, Metatranscriptomic sequencing analysis, Metagenomic sequencing analysis, Phylogenetics
Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa
Tools (4):
BLASTN, EMBOSS, Clustal W, WebLogo
Topics (3):
WGS analysis, De novo sequencing analysis, Genome annotation
Genome Wide Identification and Evolution of HECT Genes in Soybean
Tools (5):
Circos, MUSCLE, trimAl, PAML, WebLogo
Topics (2):
De novo sequencing analysis, Glycine max
A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters
Tools (5):
WebLogo, Clustal W, PHYLIP, iTOL, HMMER
Topics (2):
WGS analysis, De novo sequencing analysis
Natural HCV variants with increased replicative fitness due to NS3 helicase mutations in the C terminal helix α18
Tools (3):
MUSCLE, SeaView, WebLogo
Topics (8):
De novo sequencing analysis, Genome annotation, Hepacivirus C, Classical swine fever virus, Hepatitis, Flaviviridae Infections, Hepatitis C, Amino Acids
The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline adapted archaeon
Tools (3):
Gaggle, MEME, WebLogo
Topics (2):
De novo sequencing analysis, Genome annotation
Rapid, low input, low bias construction of shotgun fragment libraries by high density in vitro transposition
Tools (3):
BWA, Newbler, seqLogo
Topics (3):
WGS analysis, De novo sequencing analysis, Homo sapiens
Expression and evolutionary divergence of the non conventional olfactory receptor in four species of fig wasp associated with one species of fig
Tools (4):
Clustal W, WebLogo, EMBOSS, MEGA
Topics (2):
WGS analysis, De novo sequencing analysis
The architecture of ArgR DNA complexes at the genome scale in Escherichia coli
Tools (4):
CLC Genomics Workbench, BioProspector, MEME Suite, WebLogo
Topics (1):
De novo sequencing analysis