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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]].
==History==
>CY003854.1 Influenza A virus (A/mallard/Alberta/77/1977(H2N3)) segment 1, complete sequence
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.
AGCGAAAGCAGGTCAAATATATTCAATATGGAGAGAATAAAAGAACTAAGAGATCTAATGTCACAGTCCC
GCACCCGCGAGATACTCACCAAAACCACTGTGGACCACATGGCCATAATCAAAAAATACACATCAGGAAG
GCAAGAGAAGAACCCCGCACTCAGGATGAAGTGGATGATGGCAATGAAATATCCAATTACTGCAGATAAG
AGAATAATGGAAATGATTCCTGAAAGGAATGAACAAGGACAAACCCTCTGGAGCAAAACAAACGATGCCG
GCTCAGACCGAGTGATGGTATCACCTCTGGCCGTGACATGGTGGAATAGGAATGGACCAACAACAAGTAC
AGTTCACTACCCAAAGGTATATAAAACTTATTTCGAAAAAGTCGAAAGGTTGAAACACGGGACCTTTGGC
CCCGTCCACTTCAGAAATCAAGTTAAGATAAGACGGAGGGTTGACATAAACCCTGGCCACGCAGACCTCA
GTGCCAAAGAGGCACAGGATGTAATCATGGAAGTTGTTTTCCCAAATGAAGTGGGAGCTAGAATACTAAC
ATCGGAGTCACAACTGACAATAACAAAAGAGAAAAAGGAAGAACTCCAGGACTGTAAAATTGCCCCCTTG
ATGGTAGCATACATGCTAGAAAGAGAGTTGGTCCGCAAAACGAGGTTCCTCCCAGTGGCTGGTGGAACAA
GCAGTGTCTATATTGAGGTGTTGCATTTAACCCAGGGGACATGCTGGGAGCAGATGTACACTCCAGGAGG
GGAAGTGAGAAATGATGATGTTGACCAAAGCTTGATTATCGCTGCCAGGAACATAGTAAGAAGAGCAACG
GTATCAGCAGACCCACTAGCATCTCTATTGGAGATGTGCCACAGCACACAGATTGGGGGAATAAGGATGG
TAGACATCCTTCGGCAAAATCCAACAGAGGAACAAGCCGTGGACATATGCAAGGCAGCAATGGGCTTGAG
GATTAGCTCATCTTTCAGCTTTGGTGGATTCACTTTCAAAAGAACAAGCGGGTCGTCAGTTAAGAGAGAA
GAAGAAGTGCTTACGGGCAACCTTCAAACATTGAAAATAAGAGTACATGAGGGGTATGAAGAGTTCACAA
TGGTTGGGAGAAGAGCAACAGCTATTCTAAGAAAGGCAACCAGGAGATTGATCCAGCTAATAGTAAGTGG
GAGAGACGAGCAGTCAATTGCTGAAGCAATAATTGTGGCCATGGTATTTTCACAAGAGGATTGCATGATC
AAGGCAGTTCGGGGTGATCTGAACTTTGTCAATAGGGCAAATCAGCGACTGAACCCCATGCATCAACTCT
TGAGACACTTCCAAAAGGATGCAAAAGTGCTTTTCCAAAACTGGGGAATTGAACCCATTGACAATGTGAT
GGGAATGATCGGAATATTGCCCGACATGACCCCAAGTACTGAGATGTCGCTGAGGGGGATAAGAGTCAGC
AAAATGGGAGTAGATGAATACTCCAGCACAGAAAGGGTGGTGGTGAGCATTGACCGATTTTTAAGGGTTC
GGGATCAACGGGGAAACGTACTATTGTCACCCGAAGAAGTTAGCGAGACACAAGGAACGGAGAAACTGAC
AATAACTTATTCGTCATCAATGATGTGGGAGATCAATGGTCCTGAGTCGGTGTTGGTCAATACTTATCAA
TGGATCATCAGGAACTGGGAGACTGTGAAAATTCAATGGTCACAGGATCCCACAATGTTATATAATAAGA
TGGAATTCGAGCCATTTCAGTCTCTGGTCCCTAAGGCAGCCAGAGGTCAATACAGCGGATTCGTGAGGAC
ACTGTTCCAGCAGATGCGGGATGTGCTTGGAACATTTGACACTGTTCAGATAATAAAACTTCTTCCCTTT
GCTGCTGCTCCACCAGAACAGAGTAGGATGCAGTTCTCCTCCCTGACTGTGAATGTGAGAGGATCAGGAA
TGAGGATACTGGTAAGAGGCAATTCTCCAGTGTTCAATTACAACAAGGCCACCAAGAGGCTTACAGTCCT
TGGAAAAGATGCAGGTGCATTGACCGAAGATCCAGATGAAGGCACAGCTGGAGTGGAGTCTGCTGTTCTA
AGAGGATTCCTCATTTTGGGCAAAGAAGACAAGAGATATGGCCCAGCATTAAGCATCAATGAGCTGAGCA
ATCTTGCAAAAGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTGGTGTTGGTAATGAAACGGAA
ACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAGTGT
CGAATTGTTTAAAAACGACCTTGTTTCTACT
>CY003886.1 Influenza A virus (A/mallard duck/ALB/376/1985(H2N3)) segment 1, complete sequence
AGCGAAAGCAGGTCAAATATATTCAATATGGAGAGAATAAAAGAACTAAGAGATCTAATGTCACAGTCCC
GCACTCGCGAGATACTCACCAAAACCACTGTGGACCATATGGCCATAATCAAAAAATACACATCAGGAAG
GCAAGAGAAGAATCCCGCACTCAGGATGAAATGGATGATGGCAATGAAATATCCAATTACAGCGGATAAG
AGGATAATGGAGATGATTCCCGAGAGGAATGAACAAGGGCAAACCCTCTGGAGCAAAACAAATGATGCCG
GCTCAGACCGAGTGATGGTATCACCTCTGGCTGTGACATGGTGGAATAGGAATGGACCAACAACAAGTAC
AATTCACTACCCAAAGGTATATAAAACCTATTTCGAAAAGGTCGAAAGGTTAAAACATGGGACCTTTGGC
CCCGTTCACTTCAGGAATCAAGTTAAGATAAGACGGAGAGTTGACATAAACCCTGGACATGCAGACCTCA
GTGCCAAAGAGGCACAGGATGTAATCATGGAAGTTGTTTTCCCAAATGAAGTGGGGGCCAGGATATTAAC
ATCGGAGTCACAGCTGACAATAACAAAAGAGAAAAAGGAAGAACTCCAAGATTGTAAAATTGCCCCCTTG
ATGGTAGCATACATGCTAGAAAGAGAGTTAGTCCGCAAAACGAGGTTCCTCCCAGTGGCTGGTGGAACAA
GCAGTGTTTATATTGAGGTGTTGCATTTGACCCAGGGAACATGCTGGGAACAAATGTACACTCCAGGAGG
GGAAGTGAGAAATGATGATGTTGACCAAAGCTTAATTATCGCTGCCAGGAATATAGTAAGAAGAGCAACG
GTATCAGCAGACCCACTAGCGTCTCTATTGGAGATGTGCCACAGCACACAGATTGGTGGAATAAGGATGG
TAGACATCCTTAGGCAGAATCCAACAGAGGAACAAGCCGTGGATATATGCAAGGCGGCAATGGGCTTGAG
GATTAGCTCATCTTTCAGCTTCGGTGGATTCACTTTTAAAAGAACAAGTGGGTCGTCAGTCAAAAGAGAA
GAAGAAGTGCTTACGGGCAACCTTCAAACACTGAAAATAAGAGTGCATGAGGGGTATGAAGAATTCACAA
TGGTTGGGAGAAGAGCAACAGCTATTCTCAGGAAGGCAACCAGGAGATTGATTCAGCTAATAGTCAGTGG
GAGAGATGAACAGTCAATTGCTGAAGCAATAATTGTAGCTATGGTATTTTCACAAGAGGATTGCATGATC
AAGGCAGTTCGGGGTGATCTGAACTTTGTCAATAGAGCAAACCAGCGACTGAACCCCATGCATCAACTCT
TGAGACATTTCCAAAAGGATGCAAAAGTGCTTTTCCAAAATTGGGGAATTGAACCCATTGACAATGTGAT
GGGAATGATCGGAATACTACCCGACATGACCCCAAGTACTGAGACGTCATTGAGAGGGATAAGAGTCAGC
AAAATGGGAGTGGATGAATACTCCAGCACAGAGAGAGTGGTGGTGAGCATTGACCGTTTTTTAAGGGTTC
GGGATCAACGGGGAAACGTACTATTGTCACCTGAAGAAGTCAGCGAGACGCAAGGGACGGAAAAGTTGAC
AATAACTTACTCATCATCAATGATGTGGGAGATCAATGGTCCTGAATCAGTGTTGGTCAATACTTACCAG
TGGATCATCAGAAACTGGGAGACTGTGAAAATTCAATGGTCACAGGATCCCACAATGTTGTACAATAAGA
TGGAATTCGAGCCATTTCAGTCTCTGGTCCCTAAGGCAGCTAGAGGTCAATACAGCGGATTCGTGAGGAC
GCTGTTCCAACAAATGCGGGATGTGCTTGGAACATTTGACACTGTTCAGATAATAAAACTTCTCCCCTTT
GCTGCTGCCCCACCAGAACAGAGTAGGATGCAGTTCTCCTCCTTGACTGTGAATGTAAGAGGATCAGGAA
TGAGGATACTGGTAAGAGGCAACTCTCCAGTGTTCAATTACAACAAGGCCACCAAGAGGCTTACAGTCCT
CGGGAAGGATGCAGGTGCATTAACTGAAGACCCAGATGAAGGCACAGCTGGAGTGGAATCTGCTGTTCTG
AGAGGATTCCTCATTTTGGGCAAAGAAGACAAGAGATATGGCCCAGCATTGAGCATCAATGAGCTGAGCA
ATCTTGCAAAAGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTGGTGTTGGTAATGAAACGGAA
ACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGGATTCGGATGGCCATCAATTAGTGT
CGAATTGTTTAAAAACGACCTTGTTTCTACT
== Interpretation ==
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