Bird 10K genes Track Settings
 
Bird 10K gene annotation

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Bird 10K Gene Tracks

Description

This track shows the Bird 10K annotation of protein-coding genes on all 363 avian genomes in the hub.

Methods

These genes were created via a homology-based projection from two gene sets: a “primary” gene set based on Ensembl(Aken et al. 2017) version 85 annotations for chicken and zebra finch, as well as a “secondary” gene set based on human Ensembl 85 annotations as well as avian transcriptome data. These gene sets were aligned to each genome using tblastn(Altschul et al. 1990) and refined using GeneWise(Birney, Clamp, and Durbin 2004). Further filtering removed highly duplicated genes.

Credits

The Bird 10K consortium generated these gene annotations. Please contact the corresponding authors for the data release, Guojie Zhang and Benedict Paten with questions.

References

Aken, Bronwen L., Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, et al. 2017. “Ensembl 2017.” Nucleic Acids Research 45 (D1): D635–D642. https://doi.org/10.1093/nar/gkw1104.

Altschul, Stephen, Warren Gish, Webb Miller, Eugene Myers, and David Lipman. 1990. “Basic local alignment search tool.” J. Mol. Biol. 215: 403–10.

Birney, Ewan, Michele Clamp, and Richard Durbin. 2004. “GeneWise and Genomewise.” Genome Research 14 (5): 988–95.