Gene Model Check Dot Plot Analysis

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akleinschmit
Posts: 4
Joined: Tue Jun 19, 2012 9:26 pm

Gene Model Check Dot Plot Analysis

Post by akleinschmit » Thu Nov 01, 2012 3:18 am

My students and I were wondering if the labeled line (red arrow) in the dot plot below can be attributed to a simple short duplication (circled in the alignment below)? We performed a BLASTx search of the sequences involved to look for a potential duplication candidate with out much luck and spotted the 3AA by eye.

Is there a better way of analyzing dot plots? For something as small as the line in question; would a more experienced annotator spend any time on it?
Attachments
fd102C-PA Gene Model Checker.PNG
fd102C-PA Gene Model Checker.PNG (57.31 KiB) Viewed 5318 times
fd102C-PA Alignment.PNG
fd102C-PA Alignment.PNG (35.6 KiB) Viewed 5318 times

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Gene Model Check Dot Plot Analysis

Post by wleung » Thu Nov 01, 2012 4:20 pm

In general, we expect to find some short spurious matches in the dot plot. Some of these matches can occur by chance and others can be attributed to repetitive or low complexity sequences. In fact, this is one of the reasons why we use the BLAST E-value threshold and the low complexity filter to try to minimize the number of spurious matches.

In this case, the gene model is likely to be correct because fd102C consists of only a single exon in D. melanogaster and the later part of the alignment (following the deletions in the submitted model) is highly conserved.

akleinschmit
Posts: 4
Joined: Tue Jun 19, 2012 9:26 pm

Re: Gene Model Check Dot Plot Analysis

Post by akleinschmit » Thu Nov 01, 2012 5:34 pm

Sounds good. Thank you for your insight Wilson :)

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