BME 130 – Genomes

Lecture 2

Mapping Genomes

Genomics in the news

Scooped. Stephan Schuster's rivals beat him to the punch last week with announcements about the Tasmanian devil (top right) and cacao genomes prior to publication.CREDITS (CLOCKWISE FROM LEFT): PSU; VANESSA M. HAYES/JCVI; GETTY IMAGES/ISTOCKPHOTO

http://www.sciencemag.org/cgi/content/full/329/5999/1585/F1

Figure 3.1 Genomes 3 (© Garland Science 2007)

Figure 3.2a Genomes 3 (© Garland Science 2007)

Repeat content of human

item count 5,298,130

item bases1,465,724,774

(50.59%)

item total1,467,396,988

(50.65%)

smallest item 6

average item 277

biggest item 160,602

smallest score

21

average score 1,417

biggest score 75,230

RepeatMasker (rmsk) Summary Statistics

Figure 3.3 Genomes 3 (© Garland Science 2007)

A map is useful for assembly, no matter how it’s done

Figure 3.4 Genomes 3 (© Garland Science 2007)

Restriction fragment length polymorphisms

Figure 3.5a Genomes 3 (© Garland Science 2007)

Figure 3.5b Genomes 3 (© Garland Science 2007)

Figure 3.6a Genomes 3 (© Garland Science 2007)

Figure 3.6b Genomes 3 (© Garland Science 2007)

Figure 3.7 Genomes 3 (© Garland Science 2007)

Single nucleotide polymorphisms

dbSNP growth

Currently (dbSNPv131): 32,017,159 human SNPs in dbSNP!

Various ways to type SNPs (genotype)

Figure 3.8a Genomes 3 (© Garland Science 2007)

Figure 3.8b Genomes 3 (© Garland Science 2007)

Technical Note 3-1 Figure T3.2 Genomes 3 (© Garland Science 2007)

Figure 3.9a Genomes 3 (© Garland Science 2007)

Figure 3.9b Genomes 3 (© Garland Science 2007)

Figure 3.9c Genomes 3 (© Garland Science 2007)

Genes as markers

Figure 3.13 Genomes 3 (© Garland Science 2007)

Figure 3.12 part 2 of 2 Genomes 3 (© Garland Science 2007)

Table 3.2 Genomes 3 (© Garland Science 2007)

Establishing order of genes known to be linked – a

genetic map

Figure 3.22a Genomes 3 (© Garland Science 2007)

No test crosses in humans, but…

Figure 3.22b Genomes 3 (© Garland Science 2007)

Figure 3.22c Genomes 3 (© Garland Science 2007)

Figure 3.25 Genomes 3 (© Garland Science 2007)

Figure 3.27 Genomes 3 (© Garland Science 2007)

Generating a restriction map

Figure 3.27 part 1 of 3 Genomes 3 (© Garland Science 2007)

Figure 3.27 part 2 of 3 Genomes 3 (© Garland Science 2007)

Figure 3.27 part 3 of 3 Genomes 3 (© Garland Science 2007)

Figure 3.34 Genomes 3 (© Garland Science 2007)

FISH map (Fluorescence in situ hybridization)

Figure 3.33 Genomes 3 (© Garland Science 2007)

Figure 3.35 Genomes 3 (© Garland Science 2007)

Figure 3.35 Genomes 3 (© Garland Science 2007)

Figure 3.36 Genomes 3 (© Garland Science 2007)

Figure 3.37a Genomes 3 (© Garland Science 2007)

Figure 3.37b Genomes 3 (© Garland Science 2007)

Figure 3.39 Genomes 3 (© Garland Science 2007)