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Gene Model Check Dot Plot Analysis

Posted: Thu Nov 01, 2012 3:18 am
by akleinschmit
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?

Re: Gene Model Check Dot Plot Analysis

Posted: Thu Nov 01, 2012 4:20 pm
by wleung
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.

Re: Gene Model Check Dot Plot Analysis

Posted: Thu Nov 01, 2012 5:34 pm
by akleinschmit
Sounds good. Thank you for your insight Wilson :)