## Description

This track contains alignments of predicted transcripts from the DOE Joint Genome Institute (JGI) to the $organism genome.

## Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks.

The track description page offers the following filter and configuration options:

- Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison of gene predictions. Click the Help on codon coloring link on the track description page for more information about this feature.

## Methods

Predicted peptides from JGI were aligned to their predicted transcripts using the blat program to establish the coding portion of the transcript. The transcripts were then aligned to the $organism genome using blat. For more information about this assembly and an analysis of the euchromatic regions of the genome, see Dehal, P. et al. (2002) in the References section below.

## Credits

The $organism predicted transcripts and peptides were provided by JGI. Blat was written by Jim Kent.

## References

Dehal, P. et al. The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins. Science. 298(5601):2157-67 (2002).

Kent, W.J. BLAT - the BLAST-like alignment tool. Genome Res. 12(4), 656-664 (2002).