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Number of exons

Posted: Tue Apr 29, 2014 10:35 pm
by drevie
In one or two cases, students seem to have found different numbers of exons shown by the browser, GeneModelChecker, and/or GeneRecordFinder. For example, the browser may show 4 exons and the GeneModelChecker expects 5. Is one of them slightly out of sync compared to the others regarding the D. melanogaster build?

Re: Number of exons

Posted: Wed Apr 30, 2014 12:16 am
by wleung
The blastx track on the genome browser shows the alignments between the D. melanogaster proteins and the contig sequence. The boxes in the blastx track correspond to regions of the contig that is similar to a D. melanogaster protein (i.e. an alignment block). In many cases, the alignment blocks would correspond to the individual exons. However, blastx could have merged adjacent exons together into a single alignment block or split a single exon into multiple alignment blocks. Consequently, your students should not use the blastx track on the Genome Browser to infer the D. melanogaster gene structure. This is also the main rationale for performing the exon-by-exon BLAST searches in order to map the individual exons.

All the resources on the GEP Web Framework are synchronized to the same FlyBase annotation release at the beginning of every semester. Hence the Gene Model Checker, Gene Record Finder, and Annotation Files Merger should all be consistent with each other. However, because FlyBase produces a new annotation release every 6-8 weeks, some of the D. melanogaster gene records on the GEP Web Framework could be out of date. In addition, there are also instances where the gene structure of the ortholog has changed (i.e. novel introns, merged adjacent coding exons).

Re: Number of exons

Posted: Wed Apr 30, 2014 3:13 pm
by drevie
Thanks. I believe the problems are mostly between Flybase and GeneModelChecker, but the browser differences also occur. I've been telling them to double check all the differences in the dot plot, and ignore the warning if they have checked to make sure they don't have an extra or missing exon.