## Description

This track shows AceView gene models constructed from mRNA, EST and genomic evidence by Danielle and Jean Thierry-Mieg and Vahan Simonyan using the Acembly program.

## Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. Gene models that fall into the "main" prediction class are displayed in purple; "putative" genes are displayed in pink.

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

- Gene Class filter: Select the main or putative option to filter the display by prediction class.
- 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 "Codon coloring help" link on the track description page for more information about this feature.

## Methods

AceView attempts to find the best alignment of each mRNA/EST against the genome, and clusters the alignments into the least possible number of alternatively spliced transcripts. The reconstructed transcripts are then clustered into genes by simple transitive contact. To see the evidence that supports each transcript, click the "Outside Link" on an individual transcript's details page to access the NCBI AceView web site.

Each AceView transcript model has a gene cluster designation (alternate name) that is categorized into a prediction class of either main or putative.

Prediction Class: main
Class of genes that includes the protein coding genes (defined here by CDS > 100 amino acids) and all genes with at least one well-defined standard intron, i.e., an intron with a GT-AG or GC-AG boundary, supported by at least one clone matching exactly, with no ambiguous bases, and the 8 bases on either side of the intron identical to the genome. Genes with a CDS smaller than 100 amino acids are included in this class if they meet one of the following conditions: they have a NCBI RefSeq sequence (NM_#) or an OMIM identifier, or they encode a protein with BlastP homology (< 1e-3) to a cDNA-supported nematode AceView protein.

Prediction Class: putative
Class of genes that have no standard intron and do not encode CDS of more than 100 amino acids, yet may be sufficiently useful to justify not disregarding them completely. Putative genes may be of two types: either those supported by more than six cDNA clones or those that encode a putative protein with an interesting annotation. Examples include a PFAM motif, a BlastP hit to a species other than itself (< 1e-3), a transmembrane domain or other rare and meaningful domains identified by Psort2, or a highly probable localization in a cell compartment (excluding cytoplasm and nucleus).

## Credits

Thanks to Danielle and Jean Thierry-Mieg at NIH for providing this track.

## References

Thierry-Mieg D, Thierry-Mieg J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 2006;7 Suppl 1:S12.1-14.