dot plot analysis

dot plot analysis

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  Dot plot interpretationDotplot interpretation Submitted by: Shweta Kumari Roll no: 21 M.Sc Bioinformatics 2nd semester Session: 2014-16
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  ContentContent  Introduction  Principle  Example  Dot plot interpretation  Analysisof dot plot matrix  Identical sequence  Direct repeat  Inverted repeat  Palindromic sequence  Frame shifts  Low complexity region  Application  Limitation  Dot plot software  References
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  IntroductionIntroduction  In bioinformatics adot plot is a graphical method that allows the comparison of two biological sequences and identify regions of close similarity between them.  Introduced by GIBBS and MCLNTYE in 1970.  It is the one way to visualize that similarity between two protein and nucleotide sequences by uses a similarity matrix.
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  PrinciplePrinciple  Dot plot aretwo dimensional graphs, showing a comarision of two sequences.  The principle used to generate the dot plot is: The top X and the left y axes of a rectangular array are used to represent the two sequences to be compared.  Calculation: Matrix • Columns = residues of sequence 1 • Rows = residues of sequence 2  A dot is plotted at every co-ordinate where there is similarity between the bases.
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  ExampleExample Seq 1: TWILIGHTZONE Seq2: MIDNIGHTZONE Matrix= 12 * 12  A dot is plotted at every co-ordinate where there is similarity between the bases.
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  Dot plot interpretationDotplot interpretation Seq1: ATGATAT Seq2: ATGATAT
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  Analysis of dotplot matrixAnalysis of dot plot matrix  Region of similarity appears as diagonal run of dots.  Principal diagonal shows identical sequence.  Global and local alignment are shown.  Multiple diagonal indicate repeatation  Reverse diagonal (perpendicular to diagonal) indicate INVERSION.  Reverse diagonal crossing diagonal (X) indicate PALINDROMES.  Formation of box indicate the low complexity region.
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  Identical sequenceIdentical sequence  Theseare the two identical sequences:  Seq1: MALWGRL  Seq2: MALWGRL
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  Direct repeatDirect repeat
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  Inverted repeatInverted repeat Aninverted repeat is sequence of nucleotides followed downstream by its reverse complement. Inverted repeat: abcdeedcbafghijklmno
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  Palindromic sequencesPalindromic sequences Apalindromic sequence is a nucleic acid sequence (DNA or RNA) tha is same whether read 5' to 3' on one strand or 5' to 3' on the complementary strand with which it forms a double helix.
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  Frame shiftsFrame shifts Frameshifts in a nucleotide sequence can occur due to insertions, deletions or mutations. 1. Deletion of nucleotides 2.Insertion of nucleotides 3.Mutation (out of frame)
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  Low cmplexity regionLowcmplexity region  Low-complexity regions in sequences can be found as regions around the diagonal all obtaining a high score. Low complexity regions are calculated from the redundancy of amino acids within a limited region [Wootton and Federhen,1993].
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  ApplicationApplication  Shows the allpossible alignment between two nucleic acid and amino acid sequences.  All kind of local and global aligment can be traped.  Help to recognise large region of simiarity.  To find self base pairing of RNA (eg, tRNA) by comparing a sequence to itself complemented and reverse.  An excellent approach for finding sequence transposition.  To find the location of genes between two genomes.  To find the non sequential alignment.
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  LimitationLimitation  For longer sequence,memory required for the graphical representation is very high. So long sequnece can not be aligned.  Lots of insignifcant matches makes it noisy (so many off diagonal appear).  Time required to compare two sequences is proportional to the product of length of the squences time of the search window.  i.e, higher efficiency of short sequence.  Low efficiency of long sequence.
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  Dot plot softwareDotplot software  GCG is a commercial software, hence not possible to use all the time.  Instead of this, we can use the EMBOSS package, which are followig:  Dotmatcher  Dotpath  Polydot  Dottup (http://emboss.bioinformatics.nl/cgi-bin/emboss/dottup)
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  ReferencesReferences ● Bioinformatics Principal andApplications by Zhumur Ghosh and Bibekanand Mallick ● Bioinformatics concepts, skill & applications, second edition by S.C.Rastogi, Namita Mendriatta, Parag Rastogi  http://en.wikipedia.org/wiki/Dot_plot_%28bioinformatics%29  http://www.code10.info/index.php?option=com_content&view=ar ticle&id=64:inroduction-to-dot-plots&catid=52:cat_coding_al gorithms_dot-plots&Itemid=76  http://lectures.molgen.mpg.de/Pairwise/DotPlots/  https://ugene.unipro.ru/wiki/pages/viewpage.action?pageId=4 227426  http://www.clcsupport.com/clcgenomicsworkbench/650/Examples _interpretations_dot_plots.html