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Dotter
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.
Gepard / GEnome PAir - Rapid Dotter
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.
dotmatcher
Generates a dotplot from two input sequences. The dotplot products by dotmatcher is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence using a specified substitution matrix. The two sequences are the axes of the rectangular dotplot. Wherever there is "similarity" between a position from each sequence a dot is plotted. The threshold conditions for "similarity" are defined by the user.
seqinr
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.
dottup
Displays a wordmatch dotplot of two sequences. dottup looks for places where words (tuples) of a specified length have an exact match in both sequences and draws a diagonal line over the position of these words. This is a fast, but not especially sensitive way of creating dotplots. It is an acceptable method for displaying regions of substantial similarity between two sequences. Using a longer word (tuple) size displays less random noise, runs extremely quickly, but is less sensitive.
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