Download SWG diagrams

VectorBase genome annotation
VectorBase-EBI, European Bioinformatics
Institute, Wellcome Trust Genome
Campus, Hinxton UK
VectorBase SWG 2006
1
Overview of current annotation
system
Assembled
genome
Sequencing centre gene
predictions
VectorBase gene
predictions
Merge into canonical
set
Protein
analysis
Display on genome browser
Release to
GenBank/EMBL/DDBJ
VectorBase SWG 2006
2
Merging gene sets
Gene set
Gene set
#1
#2
Reduce to single predictions
per locus
Compare exon/intron
structures
Identical
structure
s
Compatib
Different Merge/Spli
le
structure t structures
structure
s
s
Add isoform predictions based on
EST/Peptide data
Canonical gene set
VectorBase SWG 2006
Complex
No
Map
3
Data types used for gene
prediction/validation
Protein sequences
‘Self’ (i.e. species to be
predicted)
Taxonomic splits of UniprotKB
Transcript sequences
mRNAs
ESTs
Evidence of expression
Microarray
SAGE tags
Ditags
MPSS
Proteomics data
Sequence statistics
Coding potential
Splice site prediction
VectorBase SWG 2006
4
VectorBase gene prediction pipeline
Blessed predictions
Manual annotations
(Apollo)
Community
(Genewise, Exonerate,
submissions
Apollo)
Similarity
(Genewise)
predictions
Species-specific
(Genewise)
predictions
ncRNA
(Rfam)
predictions
Transcript based
(Exonerate)
predictions
Canonic
al
predictio
ns
VectorBase SWG 2006
Protein family
(Genewise)
HMMs
Ab initio gene
(SNAP)
predictions
5
VectorBase curation database
pipeline for manual/community
annotation
Manual annotation
(Harvard)
Apoll
o
ChadoXML
Community annotation
(in collaboration with
Harvard)
Community annotation
(Community
representatives)
Curation
warehouse db
Chad
o
ChadoXML
Apoll
o
GFF3
Ensembl
Gene build db
VectorBase SWG 2006
6
Overview of current re-annotation
system
Full gene build
Partial Gene
build
Blessed genes
New gene
build
Compar
e
Species-specific gene
prediction
Curren
t gene
set
Updat
ed
gene
set
VectorBase SWG 2006
Merge
7
Comparing new gene builds with the
old one
• Use of manual annotation for validation of automated
gene build improvements
• Simple statistics (CDS length, intron size, CDS
matching TE’s)
• BRC annotation metrics
– Supporting evidence for a gene prediction
(citation,expression,orthology)
– Attachment of Standard Operating Procedures (SOPs)
VectorBase SWG 2006
8
Gene build schedules
Full gene
build
Triggers for re-annotation
4 months
• Temporal
• Data
• New EST data for
species
1 month
Partial gene
build
• New genomes
• Re-annotated genomes
VectorBase SWG 2006
9
VectorBase annotation
capacity with increased
number of genomes
Gene builds per year per genome
2 full
2 partial
1 full
3 partial
1full
2 partial
1 full
1 partial
2 genomes
Yes
Yes
Yes
Yes
3 genomes
Yes
Yes
Yes
Yes
4 genomes
No
Yes
Yes
Yes
5 genomes
No
Yes
Yes
Yes
6 genomes
No
No
Yes
Yes
7 genomes
No
No
No
Yes
8 genomes
No
No
No
No
VectorBase SWG 2006
10
Re-annotation questions
• Triggers for re-annotation
– Strict temporal triggers
• Always do a full gene build every year?
– Data triggers
• How much new data is enough?
• Knock-on effects of related species (re)annotation?
• Encouraging community submissions
– How can we get more community annotation input?
• Outreach at conferences (Roadshow)
VectorBase SWG 2006
11