Finding Finishing and Annotation Project Relationships

This is a place to ask any questions you may have about the GEP.
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dpaetkau
Posts: 28
Joined: Fri Jun 05, 2009 6:18 pm

Finding Finishing and Annotation Project Relationships

Post by dpaetkau » Sun Jun 19, 2016 6:48 pm

Hello Wilson,

How do you find a graphical relationship between the finishing and annotation projects for the same region.

Don

wleung
Posts: 179
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Finding Finishing and Annotation Project Relationships

Post by wleung » Sun Jun 19, 2016 10:41 pm

The placements of the sequence improvement and annotation projects are available through the "Finishing Projects" and "Annotation Projects" tracks on the GEP UCSC Genome Browser (under the Assembly Tracks section.

You can access the whole genome assemblies for the eight Drosophila species that have been sequenced by the modENCODE project by selecting the "April 2013 (BCM-HGSC)" assembly on the GEP UCSC Genome Browser Genome Gateway page. In most cases, you can simply enter the name of the D. melanogaster ortholog into the "search term" field to navigate to region within the whole genome assembly that contains the putative ortholog. You can then change the display modes of the "Finishing Projects" and "Annotation Projects" tracks to "pack" to determine the relationships between the finishing and annotation projects.

You can also navigate to the genomic region from which the annotation and sequence improvement projects were derived by entering the name of the project into the "search term" field. For sequence improvement projects, you can simply enter the name of the sequence improvement project (e.g., DELE8596006) into the "search term" field. For annotation projects, you will need to include a database prefix and an underscore before the contig name. The database name is listed at the end of the title at the top of the genome browser page (e.g., Dele1).
complete_project_name_search.png
complete_project_name_search.png (84.11 KiB) Viewed 219 times
For example, in order to navigate to the D. elegans Muller F element project contig10 in the D. elegans, one would enter "Dele1_contig10" into the "search term" field.

You can then download the corresponding annotation and sequence improvement projects through the GEP Data Repository.

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