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==History==
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 [[Residue_(chemistry)#Biochemistry|residues]] are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix.
== Interpretation ==
Some idea of the similarity of the two sequences can be gleaned from the number and length of matching segments shown in the matrix. Identical proteins will obviously have a diagonal line in the center of the matrix. Insertions and deletions between sequences give rise to disruptions in this diagonal. Regions of local similarity or repetitive sequences give rise to further diagonal matches in addition to the central diagonal. One way of reducing this noise is to only shade runs or '[[tuple]]s' of [[Residue_(chemistry)#Biochemistry|residues]], e.g. a tuple of 3 corresponds to three residues in a row. This is effective because the probability of matching three residues in a row by chance is much lower than single-residue matches.
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.
==Software to create dot plots==
* [http://www.csb.yale.edu/userguides/graphics/whatif/html/chap13.html ANACON] – Contact analysis of dot plots.
*[http://dgenies.toulouse.inra.fr/ D-Genies]<ref>{{Cite journal|title=D-GENIES : Dot plot large GENomes in an interactive, efficient and simple way|last=Klopp|first=Christophe|last2=Cabanettes|first2=Floréal|date=2018-02-23|language=en|doi=10.7287/peerj.preprints.26567v1}}</ref> – Specializes in interactive whole genome dotplots of large genomes
* [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|journal=Trends in Genetics|volume=16|issue=6|pages=276–277|issn=0168-9525|pmid=10827456|doi=10.1016/s0168-9525(00)02024-2}}</ref> – Web tool to generate dot plots (and part of the EMBOSS suite).
* [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.
* [https://github.com/evolvedmicrobe/dotplot dotplot] – R package to rapidly generate dot plots as either traditional or ggplot graphics.
* [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|journal=Gene|volume=167|issue=1–2|pages=GC1–10|issn=0378-1119|pmid=8566757|doi=10.1016/0378-1119(95)00714-8}}</ref> – Stand alone program to generate dot plots.
*[https://4virology.net/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|journal=Bioinformatics|language=en|volume=20|issue=2|pages=279–281|doi=10.1093/bioinformatics/btg406|pmid=14734323|issn=1367-4803}}</ref> – Java version of Dotter.
* [https://github.com/molbio-dresden/flexidot Flexidot]<ref>{{Cite journal|last=Seibt|first=Kathrin M.|last2=Schmidt|first2=Thomas|last3=Heitkam|first3=Tony|title=FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses|journal=Bioinformatics|volume=34|issue=20|pages=3575–3577|language=en|doi=10.1093/bioinformatics/bty395|pmid=29762645|date=2018-10-15}}</ref> – Customizable and ambiguity-aware dotplot suite for aesthetics, batch analyses and printing (implemented in Python).
* [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|journal=Bioinformatics|language=en|volume=23|issue=8|pages=1026–1028|doi=10.1093/bioinformatics/btm039|pmid=17309896|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.
* [http://last.cbrc.jp/ LAST] for whole-genome "split-alignment"<ref>{{Cite journal |author=Frith MC. and Kawaguchi R. |title=Split-alignment of genomes finds orthologies more accurately. |journal=Genome Biol. |volume=16 |year=2015 | pages=106 |doi=10.1186/s13059-015-0670-9 |pmid=25994148 |pmc=4464727}}</ref>.
* [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.
* [http://bioinfo.cristal.univ-lille.fr/yass/index.php yass]<ref>{{Cite journal |author=Noe L., Kucherov. G.|title=YASS: enhancing the sensitivity of DNA similarity search |journal=Nucleic Acids Research |volume=33|issue=2 |pages=W540–W543 |year=2005 |doi=10.1093/nar/gki478 |pmid=15980530 |pmc=1160238}}</ref> - Web-based tool to generate (both forward and reverse complement) dot plots from genomic alignments.
* [https://cran.r-project.org/web/packages/seqinr/index.html seqinr] – R package to generate dot 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.
* [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.]
In addition to the tools listed above, the NCBI Blast Server at https://blast.ncbi.nlm.nih.gov/Blast.cgi includes Dot Plots in its output.
==See also==
==References==
<references>
<ref name="gibbs-mcintyre">{{cite journal|firstfirst1=Adrian J.|lastlast1=Gibbs|first2=George A.|last2=McIntyre|title=The Diagram, a Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences|journal=Eur. J. Biochem.|volume=16|issue=1|year=1970|pages=1–11|doi=10.1111/j.1432-1033.1970.tb01046.x|pmid=5456129|doi-access=free}}</ref>
</references>
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