Updates

Moved Promoter and UTR files into FASTA/GenePrediction/
Pabies1.0-2000-downstream-regions.fa.gz
Pabies1.0-2000-upstream-regions.fa.gz
Pabies1.0-5000-downstream-regions.fa.gz
Pabies1.0-5000-upstream-regions.fa.gz
Pabies1.0-UTR-downstream-regions.fa.gz
Pabies1.0-UTR-upstream-regions.fa.gz

Moved Phase_Change folder contents(GFF3 and FASTA files) into GFF3/Phase_Change and FASTA/Phase_Change.
FASTA/Phase_Change
Pabies1.0-all.phase.gff3.CDS.fa.gz
Pabies1.0-all.phase.gff3.AA.fa.gz

GFF3/Phase_Change
Pabies1.0-all.phase.changed.gff3.gz

Added Best-BLAST hits to Annotation/Best-BLAST
Pabies1.0-gene_id_Potrav3.0-gene_id.txt.gz
Pabies1.0-gene_id_TAIR10-gene_id.txt.gz

Added GO, IPR domains, KEGG and singling peptide information from InterProScan into Annotation.
Pabies1.0-HC-pep.faa.IPR.GO.gz
Pabies1.0-HC-pep.faa.IPR.gz
Pabies1.0-HC-pep.faa.IPR.IPRscan.gz
Pabies1.0-HC-pep.faa.IPR.KEGG.gz
Pabies1.0-HC-pep.faa.IPR.txt.gz
Pabies1.0-LC-pep.faa.IPR.GO.gz
Pabies1.0-LC-pep.faa.IPR.gz
Pabies1.0-LC-pep.faa.IPR.IPRscan.gz
Pabies1.0-LC-pep.faa.IPR.KEGG.gz
Pabies1.0-LC-pep.faa.IPR.txt.gz
Pabies1.0-MC-pep.faa.IPR.GO.gz
Pabies1.0-MC-pep.faa.IPR.gz
Pabies1.0-MC-pep.faa.IPR.IPRscan.gz
Pabies1.0-MC-pep.faa.IPR.KEGG.gz
Pabies1.0-MC-pep.faa.IPR.txt.gz

Moved PFAM from GeneFamiles into Annotation.
Pabies1.0-gene_PFAM.txt.gz

== Update 14-02-2014 ==
Added GeneList annotation files to FTP[Nystedt_2013/GeneSpace/GenePrediction/annotation]

== Update 08-09-2013 ==
Loaded three tracks(High Confidence,Low Confidence and Medium Confidence) to GBrowse after adding name tags.

== Update 2013-10 ==
1. Restructure of the GenePrediction folder
2. We removed 1,917 genes from the HC set and reduced the number of genes from 28,354 to 26,437.
Please check the putative_non_nuclear folder for the detail information of removed genes.

|- annotation
| contains information about functional prediction of gene (GO, Pfam),
| gene family analysis, gene expression profile
|--- filtered_cds
| list of genes with both a start and a stop codons
|
|--- gene-family
| Gene family (TribeMCL) result
|
|- fasta
| CDS and protein sequences in the FASTA format based on the confidence level
| HC: high confidence -> 26,437 genes (= 28,354 - 1,917)
| MC: medium confidence -> 32,150 genes
| LC: low confidence -> 8,045 genes
|
|- gff
| Gene prediction result in GFF format
|
|- putative_non_nuclear
| Genes probably originated from following sources are moved to this folder
| 1) prokaryotic contamination, 2) zero-coverage contig
| 3) redundant contigs and 4) clear indication of chloroplast/mitochondria origin
| HC -> 1,917 gene
| MC -> 889 genes
| LC -> 1,720 genes
|

Also we have updated following datasets into ConGenIE.org and FTP (After removing this set of gene ids)

GBrowse

congenie.org/congenie/GBrowse/Pabies1.0/Gene_Prediction_Transcript_assemblies/Low-Confidence.gff3.gz
congenie.org/congenie/GBrowse/Pabies1.0/Gene_Prediction_Transcript_assemblies/Medium-Confidence.gff3.gz
congenie.org/congenie/GBrowse/Pabies1.0/Gene_Prediction_Transcript_assemblies/High-Confidence.gff3.gz
congenie.org/congenie/GBrowse/Pabies1.0/Gene_Prediction_Transcript_assemblies/Eugene.gff3.gz

BLAST

congenie.org/congenie/BLAST/Z4006_Gene_Prediction/Pabies1.0-all-cds.tar.gz
congenie.org/congenie/BLAST/Z4006_Gene_Prediction/Pabies1.0-all-pep.tar.gz
congenie.org/congenie/BLAST/Z4006_Gene_Prediction/Pabies1.0-high-confidence-cds.tar.gz
congenie.org/congenie/BLAST/Z4006_Gene_Prediction/Pabies1.0-high-confidence-pep.tar.gz
congenie.org/congenie/BLAST/Genome_Assemblies/Pabies1.0-genome-gene-only.fa.tar.gz

FASTA

congenie.org/congenie/fasta/GenePrediction/Pabies1.0-all-cds.fna.gz
congenie.org/congenie/fasta/GenePrediction/Pabies1.0-all-pep.faa.gz
congenie.org/congenie/fasta/GenePrediction/Pabies1.0-high-confidence-cds.fna.gz
congenie.org/congenie/fasta/GenePrediction/Pabies1.0-high-confidence-pep.faa.gz

== Update 2013-02 ==
The first release of spruce annotation