GEP Tools | Dot Plots and Protein Alignments
Channel: Genomics Education Partnership
Date: 2021-09-27

An introductory video on the analysis of dot plots and protein alignments, presented by GEP Virtual TA Rae Lucas. The dot plots and protein alignments presented in this video were generated from Gene Model Checker, with our reference organism being Drosophila melanogaster. We begin with an overview of protein alignments and how we interpret their various features, along with what this means for our aligned gene sequence. We then move on to reading and analyzing dot plots, a feature that correlates with protein alignments. A major feature of the dot plot includes word size, which may be manipulated by the user to increase or decrease sensitivity of the plot; we discuss this in brief and when we might use this before looking at common patterns that may appear in our plots. Such patterns discussed include repeating sequences, short tandem repeats, and inversions.

0:00 - Intro
00:32 - Reading a Protein Alignment
04:32 - Analyzing a Protein Alignment
08:39 - What is a Dot Plot & What Does it Tell Us?
10:00 - Reading a Dot Plot
11:13 - Word Size –a feature of dot plots
14:24 - Manipulating the Dot Plot using Word Size
16:55 - Reading Similarity in a Dot Plot
18:13 - Gaps due to Incorrect Splice Sites
19:44 - Repeating Sequences
21:59 - Short Tandem Repeats
23:09 - Inversions

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Spanish subtitles provided by REV.com and reviewed Mateo Antonio Lopez, GEP Virtual TA and biology student at Mount Saint Mary College, NY. 

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