BME 130 – Genomes Lecture 2 Mapping Genomes. Genomics in the news Scooped. Stephan Schuster's...
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Transcript of BME 130 – Genomes Lecture 2 Mapping Genomes. Genomics in the news Scooped. Stephan Schuster's...
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)