Description

We generated transcript predictions for the CB4856 reference using Genefinder, an ab initio gene prediction program. We have also provided a transcript prediction track derived from N2 transcript alignments to CB4856, which in most regions of high agreement between N2 and CB4856 should be a more accurate predictor of gene structure, as the N2 genome has been carefully curated over many years.

Display Conventions and Configuration

Transcript predictions are presented here in bed format; we would recommend viewing the track in "pack" display mode. Exons and introns should be visible for each transcript model, with the strand clearly displayed with arrows in intronic regions.

Methods

We ran Genefinder (version 1.1; P. Green, unpublished; -orfcutoff - 0.5 -intron3cutoff -0.5 -intron5cutoff -0.5) to provide de novo gene prediction across the CB4856 reference using the C. elegans table files. This resulted in 22,261 transcript predictions composed of 126,518 different exons. Gene models are presented here in bed format.

Credits

Please feel free to contact Owen Thompson with any questions and/or concerns regarding this or other tracks.

Thanks to Phil Green and LaDeana Hillier for their work creating Genefinder.

References

For a discussion of how the ab initio gene prediction program Genefinder has been critical to C. elegans reference annotation, consider:

Spieth J, Lawson D, Davis P, Williams G, Howe K. Overview of gene structure in C. elegans. WormBook. 2014;:1-18. PMID 25368915.