Bioinformatics and Functional Genomics, 2nd Edition

Chpter 19: The Human Genome

This page offers the web documents that are referred to in Chapter 5 of the book, as well as various resources. In Chapter 4 we discussed BLAST. This chapter covers BLAST-related approaches to database searching including position-specific scoring matrices and hidden Markov models that allow far more sensitive searches. We also discuss ways to search and align long segments of genomic DNA.

Web documents Page Description
Web Document 19-1 832 List of regions having very high recombination rates


Chapter 19 Resources
Powerpoint of the human genome lecture from November 2009
Course site for Genomics (260.605, 2nd quarter 2009-2010). This companion site includes information such as the class schedule and assignments.
Key URLs: NCBI; UCSC; Ensembl

Publications reporting the sequence of the human genomes and chromosomes
Project Reference PMID Accession
Human genome (public) International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)

11237011

 
Human genome (public, finished)

International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).

15496913

 
Human genome (Celera)

Venter, J. C., et al. The sequence of the human genome. Science 291, 1304–1351 (2001).

11181995

 
Individual diploid genome

Levy, S., et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).

17803354

 
chromosome 1

Gregory, S.G., et al.  The DNA sequence and biological annotation of human chromosome 1. Nature 441, 315-321 (2006).

16710414

NC_000001   

AC_000133

CH003496

chromosome 2

Hillier, L. W. et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434, 724-731 (2005).

15815621

NC_000002
chromosome 3

Muzny, D.M. et al. The DNA sequence, annotation and analysis of human chromosome 3. Nature 440, 1194-1198 (2006).

16641997

CM000464
chromosome 4

Hillier, L. W. et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434, 724-731 (2005).

15815621

CM000465
chromosome 5

Schmutz, J. et al. The DNA sequence and comparative analysis of human chromosome 5. Nature 431, 268-274 (2004).

15372022

CM000466
chromosome 6

Mungall, A.J. et al. The DNA sequence and analysis of human chromosome 6. Nature 425, 805-811 (2003).

14574404

CM000467
chromosome 7

Hillier, L. W. et al. The DNA sequence of human chromosome 7. Nature 424, 157-164 (2003).

12853948

CM000468
chromosome 7

 

12690205

BL000001
chromosome 8

Nusbaum, C. et al. DNA sequence and analysis of human chromosome 8. Nature 439, 331-335 (2006).

16421571

CM000469
chromosome 9

Humphray, S. J. et al. DNA sequence and analysis of human chromosome 9. Nature 429, 369-375 (2004).

15164053

CM000470

chromosome 10

Deloukas, P. et al. The DNA sequence and comparative analysis of human chromosome 10. Nature 429, 375-382 (2004).

15164054

CM000471

chromosome 11

Taylor, T. D. et al. Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature 440, 497-500 (2006).

16554811

CM000472

chromosome 12

Scherer, S. E. et al. The finished DNA sequence of human chromosome 12. Nature 440, 346-351 (2006).

16541075

 
chromosome 13

Dunham, A. et al. The DNA sequence and analysis of human chromosome 13. Nature 428, 522-528(2004).

15057823

 
chromosome 14

Heilig, R. et al. The DNA sequence and analysis of human chromosome 14. Nature 421, 601-607 (2003).

12508121

 
chromosome 15

Zody, M. C. et al. Analysis of the DNA sequence and duplication history of human chromosome 15. Nature 440, 671-675 (2006).

16572171

 
chromosome 16

Martin, J. et al. The sequence and analysis of duplication-rich human chromosome 16. Nature 432, 988-994 (2004).

15616553

 
chromosome 17

Muzny, D. M. et al. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature 440, 1045-1049 (2006).

16625196

 
chromosome 18

 

   
chromosome 19

Grimwood, J. et al. The DNA sequence and biology of human chromosome 19. Nature 428, 529-625 (2003).

15057824

 
chromosome 20

Deloukas, P., et al. The DNA sequence and comparative analysis of human chromosome 20. Nature 414, 865–871 (2001).

11780052

 
chromosome 21

Hattori, M. et al. The DNA sequence of human chromosome 21. Nature 405, 311-319 (2000).

10830953

 
chromosome 22

Dunham, I., et al. The DNA sequence of human chromosome 22. Nature 402, 489–495 (1999).

10591208

 
chromosome X

Ross, M.T. et al. The DNA sequence of the human X chromosome. Nature 434, 325-337 (2005).

15772651

 
chromosome Y      
To find accession numbers of chromosomes from 100 to 200 Mb, use the Entrez Nucleotide command txid9606[Organism:exp] 100000000:200000000[slen]. To see a list of chromosomal accession numbers, visit this NCBI site.