yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes

Abstract

Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets. yrGATE is designed to facilitate rapid and accurate annotation of emerging genomes as well as to confirm, refine, or correct currently published annotations. yrGATE is highly portable and supports different standard input and output formats. The yrGATE software and usage cases are available at http://www.plantgdb.org/prj/yrGATE.

Figure 1

The applications interface of yrGATE. Input to yrGATE is derived from either local database tables or distributed DAS sources. Output is either to local database tables or in the form of simple text or GFF3 files.

Figure 2

Novel gene annotation. This yrGATE implementation at ZmGDB presents the region 158659-162032 of Zea mays BAC gi 51315585. (a) The main Annotation Tool window contains a completed gene structure annotation. The provided transcript evidence consists of two groups of ESTs (9, circled) separated by a region with no spanning evidence, 160260-160664 (8). User defined exons have been designated in this region. The User Defined Exons Table (2) lists each exon by coordinates and source. (b) Exon 5, 160575..160721, was defined using portals to (b) GENSCAN and GeneSeqer@PlantGDB (not shown). Yellow buttons in the GENSCAN portal (b) add exons to the gene structure in the Annotation Tool (6 in panel a), which are presented pictorially (10 in panel a) for comparison with the Evidence Plot. A protein-coding region was evaluated using the portal to the (c) ORF Finder and imported into the Annotation Tool (4 in panel a) using the yellow button.

Figure 3

Community annotation review process. Individual Community Utilities are colored green in this diagram.

Figure 4

Community implementation of yrGATE at the PlantGDB Arabidopsis genome browser, AtGDB, for correction of a public annotation and for alternative splicing. This two-window screenshot depicts yrGATE annotations in the AtGDB browser. The outer window contains a genome context view of AtGDB, which has links to the yrGATE Annotation Tool and to AtGDB's Transcript View (1). The inner window contains the Transcript View, which presents a genome context graphic and sequence alignments represented in the graphic. The graphic has the following color assignments: yrGATE annotations, green; the public annotation, blue; cDNAs, light blue; ESTs, red; annotation protein coding regions, green and red triangles. The multiple sequence alignment in the lower panel of the Transcript View corresponds to the region of graphic contained within the green rectangle (2). The first exon (3) of the public annotation, At1g80810.1, is not supported by expressed sequence evidence, which instead suggests a downstream exon. There are two yrGATE community annotations, yrGATE-At1g80810-1 and yrGATE-At1g80810-2, both of which contain the first exon supported by the evidence but differ at the 3'-end, because the evidence suggests two alternatives for exon 11 (as seen in the multiple alignment display (4)).

Figure 5

yrGATE with DAS input implementation. (a) The entrance to yrGATE is a selection page where a genome and associated evidence sources are specified. Chicken chromosome 3 region 86850000-86990000 is selected. (b) EST and mRNA are primary evidence sources (3). Additionally, secondary evidence sources of published annotations are selected for comparison including RefSeq, Ensembl, Twinscan, SGP, and Geneid genes. The novel annotation, GG-yrGATE-microcephalin, is based on EST and mRNA evidence and is distinct from all published chicken annotations in this region on this strand (2). This novel annotation (4) contains a known angiopoietin gene, NM_204817 (1), on the opposite strand within its 12th intron.