Download Artemis as genome viewing and annotation tool

Sequence Analysis with Artemis
&
Artemis Comparison Tool (ACT)
South East Asian Training Course on
Bioinformatics Applied to Tropical Diseases - 2005
(Sponsored by UNDP/World Bank/WHO/TDR)
International Centre For Genetic Engineering And Biotechnology ,
New Delhi, INDIA
Workshop Overview
Overview of the genome sequencing and sequence analysis.
Demonstration of Artemis.
Hands on guided exercise in Artemis.
Demonstration of ACT .
Hands on guided exercise in ACT
Generating ACT comparison files
The Wellcome Trust Sanger Institute
•Funded by The Wellcome Trust, a registered
charity.
•Established in 1993 to begin the Human
genome project.
•First Draft (2000) complete (2003-4)
Wellcome Trust Photo Library
Data release policy:
All sequence data is released
immediately and is freely available via
the internet in order to maximise its
benefit for research.
http://www.sanger.ac.uk
ftp://ftp.sanger.ac.uk/
Wellcome Trust Photo Library
Generating the complete genome sequence
Infrastructure
Levels of automation
Colony picking
robots
Plasmid preps
robots
ABI3700
ABI3730
TOTAL:140
Automated sequencing
Each ABI reads 96 DNA
sequences at once.
The machines are run
10 times a day,
7 days a week.
Throughput of 1,200 to 1,300 96-well plates per day
± 120,000 DNA samples read each day.
Each day, the Sanger Institute reads 60 million base pairs. That’s
equal to one of the smaller human chromosomes and many times
that of an average bacterial genome.
Pathogen Sequencing Unit
http://www.sanger.ac.uk/Projects/Microbes
The Pathogen Group is funded by the Beowulf Genomics Initiative
to sequence the genomes of a wide range of small Eukaryotes and microbes.
Yeasts and Fungi:
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Aspergillus fumigatus
Candida dubliniensis
Candida parapsilosis
Protozoa:
Plasmodium falciparum X3
Plasmodium spp. X5
Leishmania spp.
Trypanosoma spp.
Eimeria
Theileria
Babesia
Bacteria:
M. tuberculosis
M. leprae
Y. pestis
S. typhi
C. Diphtheriae
Bordetella spp. x3
B. pseudomallei
S. aureus MRSA
S. aureus MSSA
E. carrotovora
Sequencing strategy
and assembly
Shotgun sequencing – strategy
DNA
Contiguous sequence
pUC clone
end sequence
physical gap
sequence gap
‘Draft sequence’
Order of contigs?
95% coverage, 4-5x depth.
‘A genome in a day’
‘15 in a month’
‘High-quality draft sequence’
Shotgun sequencing – strategy
DNA
Contiguous sequence
pUC clone
end sequence
physical gap
sequence gap
large clone
end sequence
Finished sequence: 100% coverage, 10x depth.
Repeats!!!
Shotgun assembly - Yersinia pestis
Primary
DNA sequence
Gene finders
Dotter
BlastN
tRNA scan
Repeats
rRNA
tRNA
BlastX
Pseudo-genes
Manual
curation
Genes
Primary
DNA sequence
Gene finders
Dotter
BlastN
tRNA scan
Repeats
rRNA
tRNA
Fasta
BlastP
Pfam
BlastX
Pseudo-genes
Prosite
Manual
curation
Psort
Manual
curation
Genes
SignalP
TMHMM
Annotated
sequence
PSU Projects
Organism
Database entry
Finished genome
Annotated genome
Artemis
Artemis
• Sequence viewer and analysis tool
– Visualization of sequence features
• DNA
• Six frame translation
– Perform and view analysis
• Basic analysis
• Launch more complex analysis and searches
• Import and view the results of other searches
Outline of Artemis demonstration
•
•
•
•
Artemis window features
Open a genome sequence
Changing the view
Getting around
– Goto Menu
– Navigator
– Feature Selector
• Basic analysis
– Edit a feature
– Fasta search
– Show feature plots
Artemis
Drop Down Menus
Entry Button Line
Main Sequence
View Panel
Sliders
Magnified
Sequence View
Panel
Feature Menu
Sliders
Artemis
Curating gene models in Artemis
Use of multiple lines of evidence
Curating gene models in Artemis
Use of FASTA evidence
EST sequencing & mapping
5’UTR M
intron
exon
stop
3’UTR
CAP
AAAAAAAAAA
CAP
AAAAAAAAAA
mRNA
TTTTTTTTT
cDNA
TTTTTTTTT
EST
EST
Curating gene models in Artemis
Use of EST evidence
ESTs
Curating gene models in Artemis
Use of EST evidence
Curation of gene models in Artemis
Mapping proteome fragments to genome
Curation and annotation in Artemis
Mapping InterPro domain hits to genome
Annotation of pathogen genomes at the PSU
(using ARTEMIS)
Finished sequence
Gene Finder
PHAT
Glimmer
Orpheus
FASTA
BLAST
EST
Primary gene model
InterPro scan
SignalP
Manual curation
TMHMM
t-RNA scan
HMMPfam
HMMSMART
PRINTS
PROSITE
ProDom
TIGRFAMs
Refined gene model
Functional classification (GO / Riley)
Organism-specific gene families
Comparative genomics (using ACT)
Complete Annotation
Gene model
annotation
Gene function
Top tips!
Manual annotation.
Use a several lines of evidence:
- Run several available gene finding programs
- Search programs: local (BLAST) and global (FASTA)
alignments
-Protein domains and motifs: Interpro (Pfam, prosite, SMART
etc.)
-Transmembrane / signal peptide prediction (TMHMM,
SignalP)
- Base your annotation on characterised proteins where
possible (e.g. UNIPROT entry)
- Read the literature (Pubmed entry)
Sanger Front page