Description

This track contained filtering of the TransMap evidence used for the T2T CHM13 assembly gene annotations using the CAT (Compartive Annotation Toolkit) software.

Display convention

This track follows the display conventions for gene prediction tracks.

Methods

Comparative Annotation toolkit

Genome annotation for T2T CHM13 assembly was performed using Comparative Annotation Toolkit (CAT). CAT leverages whole-genome alignments generated by Cactus to transfer annotations from one source genome to one or more target genomes. CAT also runs AUGUSTUS in both the comparative gene prediction mode and in a single-genome mode that utilizes Iso-Seq data to predict alternative isoforms. CAT then combines all of these annotation methods into a final consensus annotation set that represents orthology relationships as well as species-specific information.

Contacts

References

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE et al. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 2018 Jul;28(7):1029-1038. PMID: 29884752; PMC: PMC6028123.

Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656.

Stanke M, Steinkamp R, Waack S, Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12. PMID: 15215400; PMC: PMC441517.

Armstrong J, Hickey J, Diekhans M, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu V.D, Haussler D, Alföldi J, Lindblad-Toh K, Karlsson E, Jarvis E.D, Zhang G, Paten B. bioRxiv 730531; doi: https://doi.org/10.1101/730531