Dot plot (bioinformatics): Difference between revisions

Revision as of 15:19, 9 January 2016

Revision as of 00:02, 10 January 2016

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In [[bioinformatics]] a '''dot plot''' is a graphical method that allows the comparison of two [[Sequence (biology)|biological sequences]] and identify regions of close similarity between them. It is a type of [[recurrence plot]].

==historyHistory==

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<ref name="gibbs-mcintyre"/> and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes. For a simple visual representation of the similarity between two sequences, individual cells in the matrix can be shaded black if residues are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix.

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== External links ==

* [http://sourceforge.net/projects/genomdiff Genomdiff] &mdash;– an open source Java Dot Plot program for viruses

* [http://mips.gsf.de/services/analysis/gepard Gepard]

* [http://www.csb.yale.edu/userguides/graphics/whatif/html/chap13.html ANACON] &mdash;– Contact analysis of dot plots.

* [http://www.code10.info/index.php?option=com_content&view=category&id=52&Itemid=76 General introduction to dot plots with example algorithms] and a [http://www.code10.info/index.php?view=article&catid=50%3Acat_coding_software_serolis&id=63%3Aserolis-software-package-for-dot-plot-creation&option=com_content&Itemid=61 software tool to create small and medium size dot plots.]

* [http://myhits.isb-sib.ch/cgi-bin/dotlet Dotlet] &mdash;– provides a program allowing you to construct a dot plot with your own sequences.

* [http://ugene.unipro.ru/documentation/manual/plugins/dotplot.html UGENE Dot Plot viewer] &mdash; an– opensource Dot Plot visualizer

[[Category:Statistical charts and diagrams]]