Sequence logo generation software tools | High-throughput sequencing data analysis
Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position.
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 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.
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.
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.
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.
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.
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).
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