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Intro to genomics
Transcript of Intro to genomics
By any other word would smell as sweet.”
-- Romeo and Juliet (II, ii, 1-2)
Plant structure ontologies
For a new sequencing project
How would you start ?
and what problems
can you foresee
in a genome project
for your choice of
-The order of genes within each“block” of DNA is conserved
despite vastly different numbers & length of chromosomes
In a conserved 'block' the orientation of genes are generally conserved.
Syntenic gene pairs are most likely orthologous
(direct evolutionary counterparts by vertical descent).
orientation of transcription
Arabidopsis recombinant inbred maps
Made from the ‘performance’ or markers across 2-300 lines
Phenotype description in free text: Green dwarf. Broader leaves, glabra. Yellow seed.
Molecular function (how)
Biological Process (what)
Gale & Devos
Cat vs human synteny
Why cats ?
ACTUAL ONLINE DATA
Why sequence a genome ?
- Gene structures such as regulatory regions, splice sites, exon number,
exon length and sequence similarity (DNA and protein level) tend to be
- Intronic sequences and length tend to be less conserved
Human/mouse synteny (gene level)
Monolith databases holding DNA sequences
Genbank at NCBI
(NATIONAL CENTRE FOR BIOTECHNOLOGY INFORMATION)
EMBL (EUROPEAN MOLECULAR BIOLOGY LABORATORY)
DDBJ (DNA DATABANK OF JAPAN)
EACH DB EXCHANGES DATA DAILY
Germplasm curation - standards
Plant phenotype ontologies are
concatenated controlled vocabularies
Taken from Plant Ontology ( PO ) - e.g leaf, microspore.
With properties of that entity (size, shape, colour, etc):
Taken from the Phenotype, Attribute and Trait Ontology ( PATO ).
have now been
Practical step 1.
Do you have a model framework to ‘fix’ your genome on ?
Map your genome
Break your genome up into manageable lengths:
Tagged HTS fragments
Hairy, Hirsute, Pubescent
'Stick on' ESTs or perform RNAseq to determine transcripts.
Analyse by example (training sets) to develop in-silico predictions of unknown genes.
Submit it to a database.
GO – GENE ONTOLOGY
HOW do you sequence a genome ?
Can be cloned
Genome size ?
Linkage groups ?
of the whole genome
of an organism
Knowledge of the function of a genome
EACH SUBMISSION TO EACH DB HAS:
A unique identifier
Sequence data for entry
References and Medline/Pubmed link
Biologically relevant annotation
Genome size ?
Linkage groups ?
B Misof et al. Science 2014;346:763-767
12 DEC 2014 • SCIENCE VOL 346 ISSUE 6215
Jaillon, O., et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.
Nature 431, 946–957 (2004) doi:10.1038/nature03025
Sequence the ‘bits’
Ontologies are for Disambiguity
Simple and functional
Complex & heterogeneous
But must be practical
Gene set enrichment (GO enrichment)
Enrichment map (in Cytoscape)
E.g. reduction of dimensionality to aid visualisation: Network graphs, PCAs, GUIs.
Because humans are good at patterns but bad at raw numbers (especially big ones).
Cellular component (where)
A lot of Bioinformatics is about analysing data, storing it sensibly - and making it easy(ier) to assess.
Affordable personal Genomics
Controversial when they made associations
without a medic present...
Not natural or philosophical absolutes
We are not there yet with most (any?) eukaryote genomes
So affordable (in 2012) I got myself done.
Bioinformatics changed ~2005
Trends Genet. 2013 Jan; 29(1): 51–58.
"Using a CRISPR -Cas9 approach, Church’s team replaced 14 loci in the elephant genome with the mammoth version of those sequences."
Paleogenomics as an example of modern sequencing power