Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Analyses genomic DNA and Protein sequence. Dotter provides a tool to explore the visual appearance of this landscape, as well as a tool to examine the sequence alignment it represents. It runs linear in space so has no practical limit for the length of sequences. The user can 'play' with the min and max cutoffs until achieves the optimal separation between noise and signal. The tool can be used for displaying dot-matrices generated by other programs. The software is a part of the Seqtools toolkit.
Allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Gepard utilizes suffix arrays for rapid heuristic dotplot calculation. For large dotplots it searches exact word matches of a certain length (10 by default) from one sequence in the suffix array of the other sequence. As an arbitrary word is found in log(n) time within a suffix array this method reduces complexity of the dotplot calculation from O(m*n) to O(m * log n) (where n is the length of the longer, m the length of the shorter sequence). For small dotplots the classical window-based dotplot calculation is utilized.
Generates publication-ready figures for complex sequences. Flexidot is a multi-purpose dotplot tool for publication-ready dotplots, pairwise, handling self and all-against-all comparisons with individual and combined visualizations. This software transforms detected matches in diagonals and creates clear vector images or standard raster graphics. It suits for identification of conserved motifs in related sequences and evaluation of tandem repeat higher order structures of error-prone long reads.
Allows comparison of two genomes. D-Genies uses the nucleic sequence alignment program called minimap2, and produces dot plots for nucleic sequences. The software has been developed to process large genomes, but it is also suited for small or medium size genomes. It is able to produce a complete human vs chimpanzee genome dot plot in one hour and 10 min. D-Genies can be extended with new aligners and new alignment file formats.
Provides a set of programs for sequence alignments visualization. SeqTools is a web-based tool that is composed of three components: (i) Blixem is a browser for one-to-many alignment; (ii) Dotter offers a graphical program to compare two sequences and; (iii) Belvu allows users to view and edit multiple sequence alignments and phylogenic trees in a wide range of formats.
Compares easily virus genomes. GenomeDiff is a free, open-source software that allows to compare virus genomes visually by dotplot. It uses alignment view and compare, for example, Hiv-1 & Visna. Locate p24 within Hiv-1. This software can also be used to compare natural language texts. Finally, it exports diagram as PDF.
Makes a dot-plot with the output file from Compare or StemLoop. Dotplot(+) generates dot-plots of the points of similarity between two sequences. It calculates the minimum density in bases per 100 platen units along either axis that would allow all of the points to be plotted on a single page. The density can be selected and the software divides the plot into as many pages as it takes to plot the whole file.
Explores data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system. It offers a vectorized function to convert one-letter amino-acid code into the three-letter one, for instance "A" into "Ala", a function to converts an alignment into a matrix of characters, a function that tries to estimate the baseline value for relative fluorescence units (RFU) data from capillary electrophoresis with the heuristic that the most common value is the baseline and many others.
Compares sequences by the diagonal plot method. Dotlet is designed to be an independent platform and to run in a Web browser, thus enabling the majority of researchers to use it. Sequences can be imported by cut-and-paste (there is no built-in limit to the number of sequences that can be imported), and menus allow the user to select which two sequences to compare. Dotlet supports protein versus protein, DNA versus DNA, and mixed comparisons.
Topics (14): Genome annotation, De novo sequencing analysis, Homo sapiens, Neisseria meningitidis, Meningitis, Gram-Positive Bacterial Infections, Meningitis, Central Nervous System Infections, Central Nervous System Bacterial Infections, Gram-Positive Bacterial Infections, Gram-Positive Bacterial Infections, Meningitis, Central Nervous System Infections, Central Nervous System Bacterial Infections