.. This file is part of the OpenDSA eTextbook project. See
.. http://opendsa.org for more details.
.. Copyright (c) 2012-2020 by the OpenDSA Project Contributors, and
.. distributed under an MIT open source license.

.. avmetadata::
   :author: Bio_Batch2
   :satisfies: DNASeq
   :topic: DNASeq

Dotplot
=======

| Dotplot is a one of the simplest and oldest methods to compare two protein or nucleotide sequences and it's a visual/graphic way of looking at regions of similarity between two sequences.

**How to do this?**

* Two sequences of similar or variable length.
* Write each letter of one sequence in a row.
* Write each letter of the other sequence in column. 
* Start filling boxes where there is a letter for sequence 1 in 2 and for 2 in 1.
* The positions left blank if the letters are different.

**Advantages:**

* Good for identification of long regions of strong similarity.
* easy to make and interpret.
* can be used for any length sequence.

**Disadvantages:**

* graphical representation doesn't give information about mutation.

.. inlineav:: Dot ss
   :long_name: DNA Sequencing example Slideshow
   :links: AV/BIO/Dot.css 
   :scripts: AV/BIO/Dot.js
   :output: show

.. inlineav:: Filter ss
   :long_name: DNA Sequencing example Slideshow
   :links: AV/BIO/Filter.css 
   :scripts: AV/BIO/Filter.js
   :output: show