Phylogenetic Annotation Project

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Reference Genome Annotation Project: Purpose

Reference Genome Progress Reports

Project timeline

Reference genome web page


Reference Genome Mailing list

Conference Calls


Electronic jamborees

Gene Annotation wiki pages

  • The purpose of these pages are to allow discussions of annotation and orthology issues related to particular genes. The individual gene pages are to be created as needed.

PAINT : Software for tree annotation

The reference project group has developed a software to perform the annotations based on phylogenetic trees, PAINT.

PAINT Curation guidelines


Data availability

  • PAINT-generated GAF files are on the cvs repository :

Annotation Priorities

  • RefG annotation priorities as of September 2009 (following GOC meeting held in Cambridge). Including procedure to propose new targets.

Annotation targets

PAINT Annotation target 2014

Please contact PAINT team to have access to the document.

Nov 2013 PAINT - Apoptosis

May- Sept 2011: RefG_Heart_Development_co-curation#Heart_Development_Transcription_Annotation_Targets

February-April 2011: Apoptosis Reference Genome Targets

June-Sept 2010: Wnt_signaling_Pathway

Past Annotation targets

Lung_branching_morphogenesis_genes Annotation Progress

Panther gene lists

All PPOD clusters with at least one object from each of the twelve refG organisms

From May 2008

Target Gene List (May 2008-Jan 2010)

Selected refG target sets

  • PPOD clusters selected since April 2008
  • Manually curated target sets selected before April 2008

Target Gene List August 2006-April 2008

  • Access requires your email to be added to the system. Email Pascale if you would like to be added.
  • This spreadsheet contains links to separate spreadsheets maintained by each of the reference genome groups.

Scripts to ensure PAINT data integrity

Work in progress

Tree annotation progress

PAINT annotation SOPs

GAFs for trees-based annotations

Standard Operating Procedure for Tree-based propagation of annotations

Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements

Branding Ref.Genome Project

Ideas for publicizing Ref.Genome Annotation Data

Orthology determination

List of potentially problematic families for all vs. all BLAST methods of orthology determination

Data used to make orthology calls

reference proteomes files

At the July 2009 Quest for Orthologs meeting, it was agreed to decide upon a standard set of genomes, and compile "complete" sets of protein coding genes for each genome, and a representative protein sequence for each gene.

New gene2geneproduct file

At the April 2009 Reference Genome meeting it was decided to create a new file to replace the GP2protein file, called 'gene2geneproduct'. Specifications can be found on this page (will be added soon).

GAF file 2.0

The GAF file should contain 17 columns, and the meaning of columns 2, 12 and 17 have been modified. See that page for specifications.

Data used for Running P-POD orthology tool on the reference genomes gene set

by Kara Dolinski at Princeton - Nov2007

  • This page contains a description of the project and the requirements for providing files for the P-POD analysis.

GFF3 sequence files for reference genome MODs


Software/database development

The purpose of this page is to discuss features and requirements that would be desirable in a database used to replace the existing Google Spreadsheet system for managing target genes, their annotations and metrics.

Retired Pages

Those pages are kept as reference but the information in them is not the most current information.