Dot plot generation software tools | High-throughput sequencing data analysis
Dot plot are a graphical representation method where data is coded by dots on a simple scale. Dot plots are widely used in high-throughput sequencing to represent data and identify similarities or differences between sequences. Dot plot generation software tools propose a wide range of functionality to represent high throughput sequencing data.
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.
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.
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.
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.
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.
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.