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One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 [1] and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes.
The dot-matrix approach, which implicitly produces a family of alignments for individual sequence regions, is qualitative and conceptually simple, though time-consuming to analyze on a large scale. In the absence of noise, it can be easy to visually identify certain sequence features—such as insertions, deletions, repeats, or inverted repeats ...
First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. Generated with ClustalX.. Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.
Bioinformatics. 26 (19): 2460– 2461. doi: 10.1093/bioinformatics/btq461. PMID 20709691. publication: 2010 OSWALD OpenCL Smith-Waterman on Altera's FPGA for Large Protein Databases Protein Rucci E, García C, Botella G, De Giusti A, Naiouf M, Prieto-Matías M [11] 2016 parasail Fast Smith-Waterman search using SIMD parallelization: Both: Daily ...
DAS (Dense Alignment Surface) is based on low-stringency dot-plots of the query sequence against a set of library sequences - non-homologous membrane proteins - using a previously derived, special scoring matrix.
YASS (Yet Another Similarity Searcher) [1] [2] is a free software, [3] pairwise sequence alignment software for nucleotide sequences, that is, it can search for similarities between DNA or RNA sequences.
Dot matrix printers, computer printers that implement dot-matrix impact printing; Dot-matrix display, a type of display device; Dot plot (bioinformatics), a display convention for illustrating the alignment of two DNA or protein sequences. Dot Matrix, a character from the animated television series ReBoot; Dot Matrix, a character from the film ...
EMBOSS is a free c software analysis package developed for the needs of the molecular biology and bioinformatics user community. [1] The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.