Bioinformatics and Functional Genomics, 2nd Edition

Chapter 16: The Eukaryotic Chromosome

In Chapter 16 we discuss the eukaryotic chromosome, before focusing on the genomes of particular organisms: the fungi (Chapter 17), a range of eukaryotes from protozoans to primates (Chapter 18), and the human genome (Chapters 19 and 20). In this chapter topics include (1) General features of eukaryotic chromosomes, (2) Repetitive DNA content, (3) Gene content, (4) Regulatory regions, (5) Comparison of eukaryotic DNA, (6) Variation in chromosomal DNA, and (7) Techniques to measure chromosomal change.

 

Web document Page Description
Web Document 16-1
653
50,000 bases of genomic DNA from human chromosome 11 (used as input for RepeatMasking)
Web Document 16-2
656
Pairwise alignment between HBB and its pseudogene HBBP1
Web Document 16-3
660
Global pairwise alignment between the two segmentally duplicated blocks at the beta globin locus
Web Document 16-4
669
Definitions of regulatory elements within ORegAnno
Web Document 16-5
689
Ultraconserved elements in chicken and human genomes
Web Document 16-extra1
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15,000 bases of genomic DNA from human chromosome 11 (used as input for RepeatMasking)
Web Document 16-extra2
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15,000 bases of genomic DNA from human chromosome 11 (RepeatMasked)

 

Chapter 16 Resources
Powerpoint of the lecture (Wednesday November 11, 2009)
Course site for Genomics (260.605, 2nd quarter 2009-2010). This companion site includes information such as the class schedule and assignments.
Audio file (Genomics_ch16.wav)
Key URLs: UCSC genome browser, ORegAnno, RepeatMasker.




Chapter 16 Errata
On page 689, problem 16-3 should refer to web document 16-5 (not 16-4)