[Xenopus] New X laevis 9.1 genome annotations NOW available on Xenbase

xenbase xenbase at ucalgary.ca
Fri Jun 3 12:39:21 EDT 2016

Gene Model Annotation 1.8.3 of the X. laevis 9.1 Genome Build

The latest annotation of the X. laevis 9.1 genome is ready!  

This release only includes updating the gene symbol of existing gene models.  

The files for this annotation release, GFFs and FASTA, can be downloaded from the Xenbase FTP page, under the X. laevis genome assemblies and gene models category.  

Xenbase updates to X. laevis Gene Model Symbol Annotation: Merging and Validation

Gene model symbol annotations were merged and validated from the following sources: 

1) Xenopus Genome Consortium (XGC)

2) Xenbase (www.xenbase.org)

3) Dr. Anne-Hélène Monsoro-Burq (anne-helene.monsoro-burq at curie.fr) and Jean-Louis Plouhinec 

4) Dr. Emil Karaulanov (E.Karaulanov at imb-mainz.de). 

These combined efforts have named 27325 of the 45099 (61%) gene models, an increase of 5624 named models from the original XGC annotation.

The compendium of provisional annotation data from all groups was aggregated and analyzed to identify and verify symbol assignment to gene models.  

Annotations that were congruent between all annotators were automatically assigned.
For all other cases, each annotation was assessed to identify the human equivalent. 
For each of these annotations, a low level, automated symbol-matching synteny analysis was performed between the human and Xenopus loci. 
The symbols from up to fifteen neighbors, both upstream and downstream of the target gene model, in both species were used. 
Gene symbols that were confirmed by at least low level synteny were considered verified and were preferred over non-synteny annotations. 
In cases where a model had more than one annotation with synteny support, manual validation was used to identify the correct assignment (324 models). 
For models where no annotations had synteny support, assignments from the XGC and Xenbase were used. 
Differences between the XGC and Xenbase were resolved via manual annotation (>400 models).
All 1709 models annotated with an X. tropicalis 9.0 gene model ID are provisional and will require future work.

Any questions can be directed to Joshua Fortriede (Joshua.Fortried at cchmc.org) at Xenbase.


If Xenbase contributes to your research, please cite us in you papers. 

Cite us in your Materials and Methods section: Xenbase (http://www.xenbase.org/, RRID:SCR_003280)

Cite us in your references:  "Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes". Nucleic Acids Research, 2015, 43(D1): D756-D763. JB Karpinka, JD Fortriede, KA Burns, C James-Zorn, VG Ponferrada, J Lee, K Karimi, AM Zorn, PD Vize.

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