Dot plot (bioinformatics): Difference between revisions

Revision as of 08:55, 3 May 2018

Revision as of 10:29, 3 May 2018

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* [[Self-similarity matrix]]

== Software to create plots ==

==References==

<references>

<ref name="gibbs-mcintyre">{{cite journal|first=Adrian J.|last=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|year=1970|pages=1–11|doi=10.1111/j.1432-1033.1970.tb01046.x}}</ref>

</references>

== 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://cube.univie.ac.at/gepard Gepard] - Dot plot tool suitable for even genome scale.

* [http://cube.univie.ac.at/gepard Gepard]<ref>{{Cite journal|last=Krumsiek|first=J.|last2=Arnold|first2=R.|last3=Rattei|first3=T.|date=2007-04-15|title=Gepard: a rapid and sensitive tool for creating dotplots on genome scale|url=https://doi.org/10.1093/bioinformatics/btm039|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://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.]

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* [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.

* [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.

* [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] - Java version of Dotter.

* [http://virology.uvic.ca/virology-ca-tools/jdotter/ JDotter]<ref>{{Cite journal|last=Brodie|first=R.|last2=Roper|first2=R. L.|last3=Upton|first3=C.|date=2004-01-22|title=JDotter: a Java interface to multiple dotplots generated by dotter|url=https://doi.org/10.1093/bioinformatics/btg406|journal=Bioinformatics|language=en|volume=20|issue=2|pages=279–281|doi=10.1093/bioinformatics/btg406|issn=1367-4803}}</ref> - Java version of Dotter.

* [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://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==

<references>

<ref name="gibbs-mcintyre">{{cite journal|first=Adrian J.|last=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|year=1970|pages=1–11|doi=10.1111/j.1432-1033.1970.tb01046.x}}</ref>

</references>

[[Category:Statistical charts and diagrams]]