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Dot plots compare two sequences by organizing one sequence on the x-axis, and another on the y-axis, of a plot. When the residues of both sequences match at the same ___location on the plot, a dot is drawn at the corresponding position. Note, that the sequences can be written backwards or forwards, however the sequences on both axes must be written in the same direction. Also note, that the direction of the sequences on the axes will determine the direction of the line on the dot plot. Once the dots have been plotted, they will combine to form lines. The closeness of the sequences in similarity will determine how close the diagonal line is to what a graph showing a curve demonstrating a [[direct relationship]] is. This relationship is affected by certain sequence features such as frame shifts, direct repeats, and inverted repeats. Frame shifts include insertions, deletions, and mutations. The presence of one of these features, or the presence of multiple features, will cause for multiple lines to be plotted in a various possibility of configurations, depending on the features present in the sequences. A feature that will cause a very different result on the dot plot is the presence of low-complexity region/regions. [[Low-complexity regions]] are regions in the sequence with only a few amino acids, which in turn, causes redundancy within that small or limited region. These regions are typically found around the diagonal, and may or may not have a square in the middle of the dot plot.
==See also==▼
* [[Protein contact map]]▼
* [[Recurrence plot]]▼
* [[Self-similarity matrix]]▼
==Software to create plots==
* [https://genomevolution.org/coge/SynMap.pl SynMap] - An easy to use, web-based tool to generate dotplots for many species with access to an extensive genome database. Offered by the comparative genomics platform CoGe.▼
* [http://sourceforge.net/projects/genomdiff Genomdiff] – An open source Java dot plot program for viruses.▼
* [http://www.csb.yale.edu/userguides/graphics/whatif/html/chap13.html ANACON] – 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] – Provides a program allowing you to construct a dot plot with your own sequences.
* [http://www.bioinformatics.nl/cgi-bin/emboss/dotmatcher dotmatcher]<ref>{{Cite journal|last=Rice|first=P.|last2=Longden|first2=I.|last3=Bleasby|first3=A.|date=June 2000|title=EMBOSS: the European Molecular Biology Open Software Suite|url=https://www.ncbi.nlm.nih.gov/pubmed/10827456|journal=Trends in genetics: TIG|volume=16|issue=6|pages=276–277|issn=0168-9525|pmid=10827456}}</ref>
* [http://www.ac-nice.fr/svt/productions/html5/dotplot/index.htm?arn=true Dotplot]
* [https://github.com/evolvedmicrobe/dotplot dotplot]
* [http://sonnhammer.sbc.su.se/Dotter.html Dotter]<ref>{{Cite journal|last=Sonnhammer|first=E. L.|last2=Durbin|first2=R.|date=1995-12-29|title=A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis|url=https://www.ncbi.nlm.nih.gov/pubmed/8566757|journal=Gene|volume=167|issue=1-2|pages=GC1–10|issn=0378-1119|pmid=8566757}}</ref> – Stand alone program to generate dot plots.
* [http://virology.uvic.ca/virology-ca-tools/jdotter/ JDotter]<ref>{{Cite journal|last=Brodie|first=Ryan|last2=Roper|first2=Rachel L.|last3=Upton|first3=Chris|date=2004-01-22|title=JDotter: a Java interface to multiple dotplots generated by dotter|url=https://academic.oup.com/bioinformatics/article/20/2/279/204948|journal=Bioinformatics|language=en|volume=20|issue=2|pages=279–281|doi=10.1093/bioinformatics/btg406|issn=1367-4803}}</ref> – Java version of Dotter.
* [https://github.com/molbio-dresden/flexidot Flexidot]
* [http://cube.univie.ac.at/gepard Gepard]<ref>{{Cite journal|last=Krumsiek|first=Jan|last2=Arnold|first2=Roland|last3=Rattei|first3=Thomas|date=2007-04-15|title=Gepard: a rapid and sensitive tool for creating dotplots on genome scale|url=https://academic.oup.com/bioinformatics/article/23/8/1026/198110|journal=Bioinformatics|language=en|volume=23|issue=8|pages=1026–1028|doi=10.1093/bioinformatics/btm039|issn=1367-4803}}</ref> – Dot plot tool suitable for even genome scale.
▲* [http://sourceforge.net/projects/genomdiff Genomdiff] – An open source Java dot plot program for viruses.
* [https://www.bx.psu.edu/~rsharris/lastz/ lastz]<ref>{{Cite book|title=Improved pairwise alignment of genomic DNA. Ph.D. thesis.|last=Harris|first=R. S.|publisher=The Pennsylvania State University|year=2007|isbn=|___location=Pennsylvania|pages=}}</ref> and [http://globin.bx.psu.edu/dist/laj/ laj]
* [https://cran.r-project.org/web/packages/seqinr/index.html seqinr]
▲* [https://genomevolution.org/coge/SynMap.pl SynMap]
* [https://web.archive.org/web/20160416103836/https://ugene.unipro.ru/wiki/display/UUOUM15/Dotplot UGENE Dot Plot viewer] – Opensource dot plot visualizer.
▲* [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.]
▲* [https://cran.r-project.org/web/packages/seqinr/index.html seqinr] - R package to generate dot plots.
▲* [https://github.com/evolvedmicrobe/dotplot dotplot] - R package to rapidly generate dot plots as either traditional or ggplot graphics.
▲==See also==
▲* [http://www.bioinformatics.nl/cgi-bin/emboss/dotmatcher dotmatcher]<ref>{{Cite journal|last=Rice|first=P.|last2=Longden|first2=I.|last3=Bleasby|first3=A.|date=June 2000|title=EMBOSS: the European Molecular Biology Open Software Suite|url=https://www.ncbi.nlm.nih.gov/pubmed/10827456|journal=Trends in genetics: TIG|volume=16|issue=6|pages=276–277|issn=0168-9525|pmid=10827456}}</ref> - Web tool to generate dot plots.
▲* [[Protein contact map]]
▲* [[Recurrence plot]]
▲* [http://www.ac-nice.fr/svt/productions/html5/dotplot/index.htm?arn=true Dotplot], easy (educational) HTML5 tool to generate dot plots from RNA sequences.
▲* [[Self-similarity matrix]]
▲* [https://www.bx.psu.edu/~rsharris/lastz/ lastz]<ref>{{Cite book|title=Improved pairwise alignment of genomic DNA. Ph.D. thesis.|last=Harris|first=R. S.|publisher=The Pennsylvania State University|year=2007|isbn=|___location=Pennsylvania|pages=}}</ref> and [http://globin.bx.psu.edu/dist/laj/ laj], programs to prepare and visualize genomic alignments.
▲* [https://github.com/molbio-dresden/flexidot Flexidot], customizable and ambiguity-aware dotplot suite for visual sequence analyses implemented in Python.
==References==
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