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Title: Genomes and intro genomics
Description: University notes for Genomes and intro genomics.
Description: University notes for Genomes and intro genomics.
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Introductory Genomics
Books and other resources
• Genes, B
...
– http://www
...
nlm
...
gov/books/bv
...
• Introduction to genetic analysis, Griffiths
What makes up a genome?
• Bacteria:
– chromosome(s),
– megaplasmids,
– plasmids,
– plus: lysogenic phage, mobile genetic
elements
Bacterial chromosome
• Bound by nucleoide protein, highly
condensed
• Purification introduces nicks
Organization of the bacterial
genome
• Circular with one replication
origin
Bacterial genes are
often clustered
in operons
Bacterial Genomics - a simple
circle?
E
...
7 Mb
– 6 plasmids each >50 kb totaling 1
...
9 Mb c/s, & 17 linear or
circular plasmids totalling 0
...
8 Mb and linear 2
...
0 Mb
- 2 chromosomes 2
...
RHA1
• The largest bacterial genome so far!
(04/2008)
• 9
...
1 Mb)
• 7
...
85 Mb, 240 kb
Megaplasmid, and 2 small plasmids 44
kb, 20 kb
...
Often
carry novel synthetic capabilities, confer
environmental adaptability
...
Ordered libraries
• Pre-1995, genome projects for D
...
coli, S
...
subtilis, C
...
sapiens (HGP)
relied on sequencing of clones from
restriction fragments, or cosmid clones
...
Gen
...
Griffith
Strategy requires a map!
Cut sites for restriction enzyme(s)
Digest to produce 10 fragments
of ~1,000 bp
1
2
3
4
5
6
Clone individually in vector
7
8
9
10
The set of clones becomes an
ordered library
1
2
6
7
3
8
4
5
9
10
The sequences are assembled to form a
“contig” 10 kb long
2
...
g
...
??
• First tested with H
...
6-2
...
4 million bp
• 2-3% encode genes
• Approx 97% non-coding
• 98% identical to chimp!
99
...
4
How do genomes compare?
Human
3200 Mb
±35,000 genes
Thale cress
125Mb
±25,000 genes
Nematode
97 Mb
±19,000 genes
Fruit fly
180 Mb
±14,000 genes
Yeast
Tb bacillus
12 Mb
4
...
ncbi
...
nih
...
analysis, alignment, database searching,
evolution - relatedness, protein foldingstructure
– Genome sequence annotation
• Finding ORF’s
• Predicting the function of the gene product
How are genomes annotated?
• Genes predicted by gene-finder programs
– ORFs
– Markov models
• Function transfer from homologs
– BLAST
• Identifying motifs within proteins
– pFAM, PROSITE, BLOCKS
• Comparative genomics
– COGs
Title: Genomes and intro genomics
Description: University notes for Genomes and intro genomics.
Description: University notes for Genomes and intro genomics.