1. Genome Annotation

2. Genome Annotation
Annotation is the process of adding information to DNA sequence.
The information usually has DNA coordinate.
Features could be repeats, genes, promoters, protein domains……..
Features can be linked to other databases eg Pfam/Pubmed

3. Genome Annotation Genome Databases The EMBL file format
Editing EMBL files with Artemis
The annotation process
Common pitfalls

4. Public Databases Genbank, Embl and DDBJ.
All databases update each other automatically

5. EMBL and TREMBL
Patricia Rodriguez-Tomé , Peter J. Stoehr , Graham N. Cameron and Tomas P. Flores, "The European Bioinformatics Institute (EBI) databases", Nucleic Acids Res. 24:(6-13), 1996
EMBL currently contains entries

6. EMBL File Contains: A header File containing:
Information about the sequence
Organism
Authors
References
Comments
A feature table containing
Sequence features and co-ordinates

7. Header File ID PFMAL1P4 standard; DNA; INV; 66441 BP. XX AC AL031747;
SV AL
DT 24-SEP-1998 (Rel. 57, Created)
DT 27-APR-2000 (Rel. 63, Last updated, Version 13)
DE Plasmodium falciparum DNA from MAL1P4
KW HTG; rifin; telomere; var; var-like hypothetical protein.
OS Plasmodium falciparum (malaria parasite P. falciparum)
OC Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium.
RN [1]
RA Oliver K., Bowman S., Churcher C., Harris B., Harris D., Lawson D.,
RA Quail M., Rajandream M., Barrell B.;
RT ;
RL Submitted (24-SEP-1998) to the EMBL/GenBank/DDBJ databases.
RL P.falciparum Genome Sequencing Consortium, The Sanger Centre, Wellcome
RL Trust Genome Campus, Hinxton, Cambridge CB10 1S.
Header File

8. EMBL File Feature Table
Anything that can have a cordinate on a DNA sequence.
misc_difference
misc_feature misc_recomb misc_RNA misc_signal misc_structure modified_base mRNA N_region
old_sequence polyA_signal polyA_site precursor_RNA prim_transcript
primer_bind promoter protein_bind RBS repeat_region repeat_unit rep_origin rRNA S_region satellite scRNA sig_peptide snRNA snoRNA source stem_loop STS TATA_signal terminator
attenuator C_region CAAT_signal CDS conflict D-loop D_segment enhancer exon GC_signal gene iDNA intron J_segment LTR mat_peptide misc_binding
transit_peptide tRNA unsure V_region V_segment variation 3'clip 3'UTR 5'clip 5'UTR -10_signal -35_signal

9. Feature qualifiesr Additional information about a feature
/allele="text" /citation=[number] /codon=(seq:"text",aa:<amino_acid>) /codon_start=<1 /db_xref="<database>:<identifier>" /EC_number="text" /evidence=<evidence_value> /exception="text" /function="text" /gene="text" /label=feature_label /map="text"
/note="text" /number=unquoted /product="text" /protein_id="<identifier>" /pseudo /standard_name="text" /translation="text" /transl_except=(pos:<base_range>,aa:<amino_acid>) /transl_table /usedin=accnum:feature_label

10. Features

11. Annotation in Artemis
FT CDS FT /db_xref="IPR002038" FT /gene="PfLtest.01" FT /label=PfLtest.01 FT /note="PfLtest.01. len=227aa. Asp-rich protein.Predicted FT by Genefinder, Phat and GlimmerM. Similar to Plasmodium FT falciparum hypothetical kDa protein TR:O97242 FT (EMBL:AL034558) (1114 aa) fasta scores: E(): 7.1e-21, FT % id in 196 aa." FT /product="Asp-rich hypothetical protein" FT /colour=10 FT /fasta_file="fasta/sanger_100kb.embl.seq out" FT misc_feature complement( ) FT /fasta_file="fasta/TEST100.tab.seq out" FT CDS FT /gene="PfLtest.02" FT /label=PfLtest.02 FT /note="PfLtest.02. len=556aa. Predicted by Genefinder, FT Phat and GlimmerM. Unknown hypothetical protein" FT /product="unknown hypothetical protein" FT /colour=8 FT /fasta_file="fasta/sanger_100kb.embl.seq out"

12. CDS features
CDS stands for coding sequence and is used to denote genes and pseudogenes.
These features are automatically translated on submission and the protein added to the protein databases.

13. /note
Note field contains all the evidence for a gene call……..plus anything else.
Similarity (fasta or blast)
Domain/motif information (pfam, tmhmm etc)
Unusual features (repeats, aa richness)

14. /product The name of the gene product
eg Alcohol dehydrogenase
Unless there is proof we must qualify..
Putative
Possible
Always be conservative!..
eg. Putative dehydrogenase
dehyrogenase like protein
Only piece of annotation added to the protein databases.

15. Naming protocols Hypothetical protein unknown function and no homology
Conserved hypothetical protein unknown function WITH homology
alcohol dehydrogenase like looks a bit like it, but may not be.
Putative alcohol dehydrogenase probably a alcohol dehydrogenase
Alcohol dehydrogenase this has previously been characterised and shown to be alcohol dehydrogenase in this organism.

16. /gene The gene name Only transfer a gene name if it is meaningful
Eg ADH1
Only transfer a gene name if it is meaningful
Never transfer a gene name like PfB0024.
Is it a gene family? make sure two genes have the same name.

17. Transitive Annotation
AKA annotation catastrophe
Junk in = Junk out
Miss-annotations spread through incorrect database submissions.