Contig Assembly

Abstract

The generation of a contig, by overlapping consensus segments within a region of deoxyribonucleic acid, can facilitate the identification of genes and provide the basis for structural and functional analyses. Contigs can be constructed in a directed approach using region‐specific markers or by whole‐genome analysis.

Keywords: contig; restriction mapping; bacterial artificial chromosome; cosmid, P1‐derived artificial chromosome, yeast artificial chromosome, sequence tagged site

References

Bentley DR, Pruitt KD, Deloukas P, Schuler GD and Ostell J (1998) Coordination of human genome sequencing via a consensus framework map. Trends in Genetics 14: 381–384.

Coffey AJ, Roberts RG, Green ED, et al. (1992) Construction of a 2.6‐Mb contig in yeast artificial chromosomes spanning the human dystrophin gene using an STS‐based approach. Genomics 12: 474–484.

Cohen D, Chumakov I and Weissenbach J (1993) A first‐generation physical map of the human genome. Nature 366: 698–701.

Collins JE, Cole CG, Smink LJ, et al. (1995) A high‐density YAC contig map of human chromosome 22. Nature 377: 367–379.

Coulson A, Sulston J, Brenner S and Karn J (1986) Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America 83: 7821–7825.

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

Green ED and Olson MV (1990) Chromosomal region of the cystic fibrosis gene in yeast artificial chromosomes: a model for human genome mapping. Science 250: 94–98.

Gregory SG, Howell GR and Bentley DR (1997) Genome mapping by fluorescent fingerprinting. Genome Research 7: 1162–1168.

Heding IJ, Ivens AC, Wilson J, et al. (1992) The generation of ordered sets of cosmid DNA clones from human chromosome region 11p. Genomics 13: 89–94.

McPherson JD, Marra M, Hillier L, et al. (The International Human Genome Mapping Consortium) (2001) A physical map of the human genome. Nature 409: 934–941.

Olson MV, Dutchik JE, Graham MY, et al. (1986) Random‐clone strategy for genomic restriction mapping in yeast. Proceedings of the National Academy of Sciences of the United States of America 83: 7826–7830.

Olson M, Hood L, Cantor C and Botstein D (1988) A common language for the physical mapping of the human genome. Science 245: 1434–1435.

Riles L, Dutchik JE, Baktha A, et al. (1993) Physical maps of the six smallest chromosomes of Saccharomyces cerevisiae at a resolution of 2.6 kilobase pairs. Genetics 134: 81–150.

Schuler GD (1997) Sequence mapping by electronic PCR. Genome Research 7: 541–550.

Staden R (1980) A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Research 8: 3673–3694.

Zhao S (2000) Human BAC ends. Nucleic Acids Research 28: 129–132.

Further Reading

Albertsen HM, Abderrahim H, Cann HM, et al. (1990) Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents. Proceedings of the National Academy of Sciences of the United States of America 87: 4256–4260.

Cheung VG, Nowak N, Jang W, et al. (2001) Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409: 953–958.

Green ED, Riethman HC, Dutchik JE and Olson MV (1991) Detection and characterization of chimeric yeast artificial chromosome clones. Genomics 11: 658–669.

Hattori M, Fujiyama A, Taylor TD, et al. (2000) The DNA sequence of human chromosome 21. Nature 405: 311–319.

Hoheisel JD, Maier E, Mott R, et al. (1993) High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe. Cell 73: 109–120.

Hudson TJ, Stein LD, Gerety SS, et al. (1995) An STS‐based map of the human genome. Science 270: 1945–1954.

Ioannou PA, Amemiya CT, Garnes J, et al. (1994) A new bacteriophage P1‐derived vector for the propagation of large human DNA fragments. Nature Genetics 6: 84–89.

Marra MA, Kucaba TA, Dietrich NL, et al. (1997) High throughput fingerprint analysis of large‐insert clones. Genome Research 7: 1072–1084.

Martin CH, Mayeda CA, Davis CA, et al. (1995) Complete sequence of the bithorax complex of Drosophila. Proceedings of the National Academy of Sciences of the United States of America 92: 8398–8402.

Shizuya, H, Birren B, Kim UJ, et al. (1992) Cloning and stable maintenance of 300‐kilobase‐pair fragments of human DNA in Escherichia coli using an F‐factor based vector. Proceedings of the National Academy of Sciences of the United States of America 89: 8794–8797.

Taylor K, Hornigold N, Conway D, et al. (1996) Mapping the human Y chromosome by fingerprinting cosmid clones. Genome Research 6: 235–248.

Web Links

Caltech Genome Research Laboratory. Resource for human CIT BAC libraries and BAC end information http://informa.bio.caltech.edu/idx_www_tree.html

CHORI (Children's Hospital Oakland Research Institute) BACPAC Resources. Resource for BAC and PAC genomic libraries, filters and cloning vectors of many different organisms http://www.chori.org/bacpac/

Clemson University Genomics Institute. Resource for genomic and EST libraries http://www.genome.clemson.edu/index.html

Ensembl Mouse Genome Server. Genome browser containing mouse map, sequence and analysed genome data http://www.ensembl.org/Mus_musculus/

ResGen Invitrogen Corporation. Resource for BAC, PAC and cDNA libraries from many organisms http://www.resgen.com/intro/libraries.php3

The Wellcome Trust Sanger Institute. Vectorette end rescue of bacterial clones. Outlines the vecorette bacterial clone end rescue technique and protocols http://www.sanger.ac.uk/HGP/methods/mapping/chr_walking/

UK HGMP Resource Centre. Resource of genomic YAC, BAC, PAC and cDNA libraries http://www.hgmp.mrc.ac.uk/geneservice/resources_index.html

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Gregory, Simon G(Sep 2005) Contig Assembly. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005365]