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dot plot adjustability?

Posted: Tue Apr 09, 2013 1:09 am
by cjones
Many of my students annotating ananassae are finding themselves with one or two small exons amid vast introns occupying the rest of the fosmid. If the run Gene Model Checker and look at the dot plot, its impossible to interpret if the gene that their small exon is from is large -- they get an essentially vertical line. Is there any way to instruct the GMC to only include the corresponding exon(s) from the melanogaster gene when constructing the dot plot?

Re: dot plot adjustability?

Posted: Tue Apr 09, 2013 2:34 am
by wleung
No, the Gene Model Checker does not have the option to align the submitted model against just a part of the D. melanogaster ortholog.

However, you can use the NCBI blastp program (with bl2seq) to compare parts of the protein. In addition to the protein alignment, the output from bl2seq include a dot plot. Basically, I would extract the part of the D. melanogaster protein sequence of interests and then compare it against the protein sequence of your submitted model (available under the "Peptide Sequence" tab of the Gene Model Checker).

In addition, you can use the dottup tool (part of the EMBOSS package) to generate a higher resolution dot plot.