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Apollo:
Collaborative Genome Annotation Editing
Monica Munoz-Torres, PhD | @monimunozto
Berkeley Bioinformatics Open-Source Projects
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
A workshop for the IAGC research community - 22 March, 2017
UNIVERSITY OF
CALIFORNIA
Today...
We will discuss effective ways to extract valuable
information about a genome through curation efforts.
After this workshop, you will:
• Better understand curation in the context of genome annotation:
assembled genome à automated annotation à manual annotation
• Become familiar with Apollo’s environment and functionality.
• Learn to identify homologs of known genes of interest in your newly
sequenced genome.
• Learn how to corroborate and modify automatically annotated gene
models using all available evidence in Apollo.
Experimental design, sampling
Comparative analyses
Merged
Gene Set
Manual
Annotation
Automated
Annotation
Sequencing
Assembly
Synthesis &
dissemination
Life Cycle of a Genome Sequencing Project
Knowledge
”
“NIH seeks fundamental knowledge about the
nature and behavior of living systems and the
application of that knowledge to enhance health,
lengthen life, and reduce illness and disability.
U.S. National Institutes of Health
”
“[The NSF aims to] promote and disseminate
research, creating knowledge that is valuable to
society, the economy, and politics.
Swiss National Science Foundation
Data
Red: FF0000
Extracting knowledge from data
Data
Information
South-facing traffic light at
St. Charles Ave. has turned red
Extracting knowledge from data
Data
Information
Knowledge
The light I am driving
towards has just turned red
Extracting knowledge from data
Data
Information
Knowledge
I must stop!
Extracting knowledge from data
Biocuration is a knowledge-extraction process
Figure	is	not	yet	public.	Do	not	reproduce.
biocuration.org
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Genome Curation
Marbach et al. 2011. Nature Methods | Shutterstock.com | Alexander Wild
Unlocking genomes
Good genes are required!
1. Generate gene models
• A few rounds of gene prediction.
2. Annotate gene models
• Function, expression patterns,
metabolic network memberships.
3. Manually review them
• Structure & Function.
Best representation of biology &
removal of elements reflecting
errors in automated analyses.
Functional assignments through
comparative analysis using literature,
databases, and experimental data.
Curation improves quality
Apollo
Gene Ontology
• To make accurate orthology assessments
• To accurately annotate expanded / contracted gene families
• To identify novel genes, species-specific isoforms
• To efficiently take advantage of transcriptomic analyses
Curation is valuable
Predicting & annotating
gene structures
Gene Prediction & Gene Annotation
Identification and annotation of genomic elements:
• Primarily focuses on protein-coding genes.
• Also identifies RNAs (tRNA, rRNA, long and small non-coding
RNAs (ncRNA)), regulatory motifs, repetitive elements, etc.
• Happens in 2 steps:
• Computation phase
• Annotation phase
Computation Phase (1)
1) Experimental data are aligned to the genome:
expressed sequence tags, RNA-sequencing reads, proteins.
Yandell & Ence. Nature Rev 2012 doi:10.1038/nrg3174
2) Gene predictions are generated:
2a) Ab initio: based on nucleotide sequence and composition
e.g. Augustus, GENSCAN, geneid, fgenesh, etc.
2b) Using experimental evidence: identifying domains and motifs
e.g. SGP2, JAMg, fgenesh++, etc.
Computation Phase (2)
Yandell & Ence. Nature Rev 2012 doi:10.1038/nrg3174
Gene Prediction - methods for discovery
2a) Ab initio:
- Based on DNA composition
- Deals strictly with genomic sequences
- Makes use of statistical approaches (e.g.
HMM) to search for coding regions and
typical gene signals
• E.g. Augustus, GENSCAN, geneid, fgenesh, etc.
2b) Evidence-based:
- Finds genes using either similarity searches against public
databases or other experimental data sets e.g. RNAseq.
E.g: SGP2, fgenesh++, JAMg, etc.
Gene Prediction - methods for discovery
• The single most likely coding sequence, no UTRs, no isoforms.
Computation Phase: result
• Data from experimental evidence and prediction tools are synthesized into a
reliable set of structural gene annotations.
5’ UTR 3’ UTR
Annotation Phase
Consensus Gene Sets
Gene models may be organized into sets using:
• Combiners for automatic integration of predicted sets
e.g: GLEAN, EvidenceModeler, etc.
• Tools packaged into pipelines
e.g: MAKER, PASA, Gnomon, Ensembl, etc.
Challenges
Ab initio
+ can capture species-specific or highly-divergent genes
- false positive predictions (incomplete predictions, readthrough predictions)
- not enough on its own to establish orthology
Reference-guided
+ uses reliable gene orthologs from better-annotated species
- can miss species-specific genes and other sequences
- not enough on its own to establish orthology
Some suggestions
• Hybrid reference-guided & ab initio gene prediction
• Generate transcriptomic data to confirm predictions, extend & improve
models, identify new expressed loci.
– the more tissues, the better!
• Review synteny to verify orthologous assignments
– largely manual for now.
Annotating gene functions
Attaching metadata to structural annotations for the
purpose of assigning a particular function.
• Assignments do not necessarily have to be supported by your own experimental data.
• Sequence similarity approaches must be informed and validated by evolutionary theory,
not just a score value.
Functional Annotation
Terms (classes) arranged in a graph: molecular
functions, biological processes, cellular
locations, and the relationships connecting
them all, in a species-independent manner.
Gene OntologyGeneOntology.org
1. Molecular Function
An elemental activity or task or job
• protein kinase activity
• insulin receptor activity
Insulin Receptor
Petrus et al, 2009, ChemMedChem
2. Biological Process
A commonly recognized series of events
• cell division
End of Telophase.
Lothar Schermelleh
3. Cellular Component
Where a gene product is located
• mitochondria
• mitochondrial
matrix
• mitochondrial
inner
membrane
Mitochondrion.
PaisekaScience Photo Library
Collaboratively
curating gene structures
Color	by	CDS	frame,	toggle	strands,	
set	color	scheme	and	highlights.
Upload	evidence	files	(GFF3,	BAM,	BigWig),	
add	combination and	sequence	search	tracks.
Query	the	genome	using	BLAT.
Navigate	and	zoom.
Search	for	a	gene	model	
or	a	scaffold.
User-created	annotations.
Annotator	panel.
Evidence	Tracks.
Stage	and	cell-type	
specific	transcription	
data.
Admin
Protein coding, pseudogenes, ncRNAs,
regulatory elements, variants, etc.
Collaborative, instantaneous,
web-based, built on top of JBrowse.
GenomeArchitect.org
Apollo Genome Annotation Editor
Apollo Functionality Overview
GenomeArchitect.org
Apollo
GenomeArchitect.org
Export
Apollo
GenomeArchitect.org
Collaboration in real time
Apollo Architecture
1. Select or find a region of interest (e.g. scaffold).
2. Select appropriate evidence tracks to review the genome element
to annotate (e.g. gene model).
3. Determine whether a feature in an existing evidence track will
provide a reasonable gene model to start working.
4. If necessary, adjust the gene model.
5. Check your edited gene model for integrity and accuracy by
comparing it with available homologs.
6. Comment and finish.
General process of curation
A brief refresher
Defining a gene
Consider that:
• A gene is a genomic sequence (DNA or RNA) directly encoding
functional product molecules, either RNA or protein.
• If several functional products share overlapping regions, we take the
union of all overlapping genomics sequences coding for them.
• This union must be coherent – i.e., processed separately for final
protein and RNA products – but does not require that all products
necessarily share a common subsequence.
Biorefresher
The gene: a moving target
“The gene is a union of genomic
sequences encoding a coherent
set of potentially overlapping
functional products.”
Gerstein et al., 2007. Genome Res
Biorefresher
mRNA
Although of brief existence, understanding mRNAs is absolutely crucial.
"Gene structure" by Daycd- Wikimedia Commons
Biorefresher
Reading frames
In eukaryotes, only one reading frame per section of DNA is biologically
relevant at a time: it has the potential to be transcribed into RNA and
translated into protein.
OPEN READING FRAME (ORF)
ORF = Start signal + coding sequence (divisible by 3) + Stop signal
Biorefresher
Splice sites
Splicing “signals” (from the point of view of an intron):
• 5’ end splice “signal” (site): usually GT (less common: GC)
• 3’ end splice site: usually AG
…]5’ - GT / AG - 3’[…
Alternatively bringing exons together produces more than
one protein from the same genic region: isoforms.
Biorefresher
• Introns can interrupt the reading frame of a gene by inserting a
sequence between two consecutive codons
• Between the first and second nucleotide of a codon
• Or between the second and third nucleotide of a codon
Exons and Introns
Biorefresher
Obstacles to transcription and translation
• Premature Stop codons in the message, are possible. A process called
non-sense mediated decay checks and corrects them to avoid: incomplete
splicing, DNA mutations, transcription errors, and leaky scanning of
ribosome – which can cause changes in the reading frame (frame shifts).
• Insertions and deletions (indels) can cause frame shifts when the indel is not
divisible by three. As a result, the peptide can be abnormally long, or
abnormally short – depending when the first in-frame Stop signal is located.
Biorefresher
Berkeley Bioinformatics Open-Source Projects,
Environmental Genomics & Systems Biology,
Lawrence Berkeley National Laboratory
Suzanna Lewis & Chris Mungall
Seth Carbon (Noctua / AmiGO)
Nathan Dunn* (Apollo)
Monica Munoz-Torres (Apollo / GO)
Jeremy Nguyen Xuan (Monarch Initiative)
Funding
• Work for GOC is supported by NIH grant 5U41HG002273-14 from
NHGRI.
• Apollo is supported by NIH grants 5R01GM080203 from NIGMS,
and 5R01HG004483 from NHGRI.
• BBOP is also supported by the Director, Office of Science,
Office of Basic Energy Sciences, of the U.S. Department of
Energy under Contract No. DE-AC02-05CH11231
For your attention, Thank You.
berkeleybop.org
Collaborators
• Ian Holmes, Eric Yao, UC Berkeley (JBrowse)
• Chris Elsik, Deepak Unni, U of Missouri (Apollo)
• Paul Thomas, USC (Noctua)
• Monica Poelchau, USDA/NAL (Apollo)
• Gene Ontology Consortium
• i5k Community
UNIVERSITY OF
CALIFORNIA

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Curation Introduction - Apollo Workshop

  • 1. Apollo: Collaborative Genome Annotation Editing Monica Munoz-Torres, PhD | @monimunozto Berkeley Bioinformatics Open-Source Projects Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory A workshop for the IAGC research community - 22 March, 2017 UNIVERSITY OF CALIFORNIA
  • 2. Today... We will discuss effective ways to extract valuable information about a genome through curation efforts.
  • 3. After this workshop, you will: • Better understand curation in the context of genome annotation: assembled genome à automated annotation à manual annotation • Become familiar with Apollo’s environment and functionality. • Learn to identify homologs of known genes of interest in your newly sequenced genome. • Learn how to corroborate and modify automatically annotated gene models using all available evidence in Apollo.
  • 4. Experimental design, sampling Comparative analyses Merged Gene Set Manual Annotation Automated Annotation Sequencing Assembly Synthesis & dissemination Life Cycle of a Genome Sequencing Project
  • 5.
  • 7. ” “NIH seeks fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce illness and disability. U.S. National Institutes of Health
  • 8. ” “[The NSF aims to] promote and disseminate research, creating knowledge that is valuable to society, the economy, and politics. Swiss National Science Foundation
  • 10. Data Information South-facing traffic light at St. Charles Ave. has turned red Extracting knowledge from data
  • 11. Data Information Knowledge The light I am driving towards has just turned red Extracting knowledge from data
  • 13. Biocuration is a knowledge-extraction process Figure is not yet public. Do not reproduce. biocuration.org IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE IMAGE IS NOT PUBLIC – DO NOT REPRODUCE
  • 15. Marbach et al. 2011. Nature Methods | Shutterstock.com | Alexander Wild Unlocking genomes
  • 16. Good genes are required! 1. Generate gene models • A few rounds of gene prediction. 2. Annotate gene models • Function, expression patterns, metabolic network memberships. 3. Manually review them • Structure & Function.
  • 17. Best representation of biology & removal of elements reflecting errors in automated analyses. Functional assignments through comparative analysis using literature, databases, and experimental data. Curation improves quality Apollo Gene Ontology
  • 18. • To make accurate orthology assessments • To accurately annotate expanded / contracted gene families • To identify novel genes, species-specific isoforms • To efficiently take advantage of transcriptomic analyses Curation is valuable
  • 20. Gene Prediction & Gene Annotation Identification and annotation of genomic elements: • Primarily focuses on protein-coding genes. • Also identifies RNAs (tRNA, rRNA, long and small non-coding RNAs (ncRNA)), regulatory motifs, repetitive elements, etc. • Happens in 2 steps: • Computation phase • Annotation phase
  • 21. Computation Phase (1) 1) Experimental data are aligned to the genome: expressed sequence tags, RNA-sequencing reads, proteins. Yandell & Ence. Nature Rev 2012 doi:10.1038/nrg3174
  • 22. 2) Gene predictions are generated: 2a) Ab initio: based on nucleotide sequence and composition e.g. Augustus, GENSCAN, geneid, fgenesh, etc. 2b) Using experimental evidence: identifying domains and motifs e.g. SGP2, JAMg, fgenesh++, etc. Computation Phase (2) Yandell & Ence. Nature Rev 2012 doi:10.1038/nrg3174
  • 23. Gene Prediction - methods for discovery 2a) Ab initio: - Based on DNA composition - Deals strictly with genomic sequences - Makes use of statistical approaches (e.g. HMM) to search for coding regions and typical gene signals • E.g. Augustus, GENSCAN, geneid, fgenesh, etc.
  • 24. 2b) Evidence-based: - Finds genes using either similarity searches against public databases or other experimental data sets e.g. RNAseq. E.g: SGP2, fgenesh++, JAMg, etc. Gene Prediction - methods for discovery
  • 25. • The single most likely coding sequence, no UTRs, no isoforms. Computation Phase: result
  • 26. • Data from experimental evidence and prediction tools are synthesized into a reliable set of structural gene annotations. 5’ UTR 3’ UTR Annotation Phase
  • 27. Consensus Gene Sets Gene models may be organized into sets using: • Combiners for automatic integration of predicted sets e.g: GLEAN, EvidenceModeler, etc. • Tools packaged into pipelines e.g: MAKER, PASA, Gnomon, Ensembl, etc.
  • 28. Challenges Ab initio + can capture species-specific or highly-divergent genes - false positive predictions (incomplete predictions, readthrough predictions) - not enough on its own to establish orthology Reference-guided + uses reliable gene orthologs from better-annotated species - can miss species-specific genes and other sequences - not enough on its own to establish orthology
  • 29. Some suggestions • Hybrid reference-guided & ab initio gene prediction • Generate transcriptomic data to confirm predictions, extend & improve models, identify new expressed loci. – the more tissues, the better! • Review synteny to verify orthologous assignments – largely manual for now.
  • 31. Attaching metadata to structural annotations for the purpose of assigning a particular function. • Assignments do not necessarily have to be supported by your own experimental data. • Sequence similarity approaches must be informed and validated by evolutionary theory, not just a score value. Functional Annotation
  • 32. Terms (classes) arranged in a graph: molecular functions, biological processes, cellular locations, and the relationships connecting them all, in a species-independent manner. Gene OntologyGeneOntology.org 1. Molecular Function An elemental activity or task or job • protein kinase activity • insulin receptor activity Insulin Receptor Petrus et al, 2009, ChemMedChem 2. Biological Process A commonly recognized series of events • cell division End of Telophase. Lothar Schermelleh 3. Cellular Component Where a gene product is located • mitochondria • mitochondrial matrix • mitochondrial inner membrane Mitochondrion. PaisekaScience Photo Library
  • 33.
  • 40. 1. Select or find a region of interest (e.g. scaffold). 2. Select appropriate evidence tracks to review the genome element to annotate (e.g. gene model). 3. Determine whether a feature in an existing evidence track will provide a reasonable gene model to start working. 4. If necessary, adjust the gene model. 5. Check your edited gene model for integrity and accuracy by comparing it with available homologs. 6. Comment and finish. General process of curation
  • 42. Defining a gene Consider that: • A gene is a genomic sequence (DNA or RNA) directly encoding functional product molecules, either RNA or protein. • If several functional products share overlapping regions, we take the union of all overlapping genomics sequences coding for them. • This union must be coherent – i.e., processed separately for final protein and RNA products – but does not require that all products necessarily share a common subsequence. Biorefresher
  • 43. The gene: a moving target “The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products.” Gerstein et al., 2007. Genome Res Biorefresher
  • 44. mRNA Although of brief existence, understanding mRNAs is absolutely crucial. "Gene structure" by Daycd- Wikimedia Commons Biorefresher
  • 45. Reading frames In eukaryotes, only one reading frame per section of DNA is biologically relevant at a time: it has the potential to be transcribed into RNA and translated into protein. OPEN READING FRAME (ORF) ORF = Start signal + coding sequence (divisible by 3) + Stop signal Biorefresher
  • 46. Splice sites Splicing “signals” (from the point of view of an intron): • 5’ end splice “signal” (site): usually GT (less common: GC) • 3’ end splice site: usually AG …]5’ - GT / AG - 3’[… Alternatively bringing exons together produces more than one protein from the same genic region: isoforms. Biorefresher
  • 47. • Introns can interrupt the reading frame of a gene by inserting a sequence between two consecutive codons • Between the first and second nucleotide of a codon • Or between the second and third nucleotide of a codon Exons and Introns Biorefresher
  • 48. Obstacles to transcription and translation • Premature Stop codons in the message, are possible. A process called non-sense mediated decay checks and corrects them to avoid: incomplete splicing, DNA mutations, transcription errors, and leaky scanning of ribosome – which can cause changes in the reading frame (frame shifts). • Insertions and deletions (indels) can cause frame shifts when the indel is not divisible by three. As a result, the peptide can be abnormally long, or abnormally short – depending when the first in-frame Stop signal is located. Biorefresher
  • 49. Berkeley Bioinformatics Open-Source Projects, Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory Suzanna Lewis & Chris Mungall Seth Carbon (Noctua / AmiGO) Nathan Dunn* (Apollo) Monica Munoz-Torres (Apollo / GO) Jeremy Nguyen Xuan (Monarch Initiative) Funding • Work for GOC is supported by NIH grant 5U41HG002273-14 from NHGRI. • Apollo is supported by NIH grants 5R01GM080203 from NIGMS, and 5R01HG004483 from NHGRI. • BBOP is also supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 For your attention, Thank You. berkeleybop.org Collaborators • Ian Holmes, Eric Yao, UC Berkeley (JBrowse) • Chris Elsik, Deepak Unni, U of Missouri (Apollo) • Paul Thomas, USC (Noctua) • Monica Poelchau, USDA/NAL (Apollo) • Gene Ontology Consortium • i5k Community UNIVERSITY OF CALIFORNIA