New X. laevis 9.2 and X. tropicalis 9.1 GFFs

Project URLs

https://gitlab.com/Xenbase/genomics/XENLA_9.2

https://gitlab.com/Xenbase/genomics/XENTR_9.1

Xenla 9.2 – Genes – 51041, named 22329

Xentr 9.1 – Genes – 34207, named 18335

To facilitate better versioning of Genome annotation files, and to provide a platform for easier community feedback and data submission, Xenbase is now housing GFF files in GitLab. Stable copies will still be available at the Xenbase FTP.

The tracks can be viewed on the Xenbase JBrowse genome browser at:

http://www.xenbase.org/common/displayJBrowse.do?data=xl9_2

and

http://www.xenbase.org/common/displayJBrowse.do?data=xt9_1

The Xenbase GFFs were created by merging the NCBI generated GFF file and the JGI/XGC submitted GFF file to Genbank. Gene exons (of non-coding genes) and CDS elements were intersected using bedtools intersect program. This was processed back up to the gene level, and recursive clustering was used to identify groups of overlapped NCBI and JGI gene models. Transcripts of gene models in clusters containing 1 NCBI gene and 1 JGI gene were merged together under a single gene model. In cases where a cluster contained 2 or more of either NCBI genes or JGI genes, each gene model was copied over individually. Unique gene models from each GFF were also copied over individually.