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Reference genome

reference genome, reference genome algorithm
A reference genome also known as a reference assembly is a digital nucleic acid sequence database, assembled by scientists as a representative example of a species' set of genes As they are often assembled from the sequencing of DNA from a number of donors, reference genomes do not accurately represent the set of genes of any single person Instead a reference provides a haploid mosaic of different DNA sequences from each donor For example, GRChg37, the Genome Reference Consortium human genome build 37 is derived from thirteen anonymous volunteers from Buffalo, New York The ABO blood group system differs among humans, but the human reference genome contains only an O allele although the other alleles are annotated

As the cost of DNA sequencing falls, and new full genome sequencing technologies emerge, more genome sequences continue to be generated Reference genomes are typically used as a guide on which new genomes are built, enabling them to be assembled much more quickly and cheaply than the initial Human Genome Project Most individuals with their entire genome sequenced, such as James D Watson, had their genome assembled in this manner For much of a genome, the reference provides a good approximation of the DNA of any single individual But in regions with high allelic diversity, such as the major histocompatibility complex in humans and the major urinary proteins of mice, the reference genome may differ significantly from other individuals Comparison between the reference build 36 and Watson's genome revealed 33 million single nucleotide polymorphism differences, while about 14 percent of his DNA could not be matched to the reference genome at all For regions where there is known to be large scale variation, sets of alternate loci are assembled alongside the reference locus

Reference genomes can be accessed online at several locations, using dedicated browsers such as Ensembl or UCSC Genome Browser

Contents

  • 1 Properties of reference genomes
    • 11 Measures of length
  • 2 Mammalian genomes
    • 21 Human reference genome
    • 22 Mouse reference genome
  • 3 Tutorials
  • 4 References
  • 5 External links

Properties of reference genomes

Measures of length

The length of a genome can be measured in multiple different ways

A simple way to measure genome length is to count the number of base pairs in the assembly

The golden path is an alternative measure of length that omits redundant regions such as haplotypes and pseudoautosomal regions It is usually constructed by layering sequencing information over a physical map to combine scaffold information It is a 'best estimate' of what the genome will look like and typically includes gaps, making it longer than the typical base pair assembly

Mammalian genomes

The human and mouse reference genomes are maintained and improved by the Genome Reference Consortium GRC, a group of fewer than 20 scientists from a number of genome research institutes, including the European Bioinformatics Institute, the National Center for Biotechnology Information, the Sanger Institute and McDonnell Genome Institute at Washington University in St Louis GRC continues to improve reference genomes by building new alignments that contain fewer gaps, and fixing misrepresentations in the sequence

Human reference genome

The human reference genome GRCh38 was released from the Genome Reference Consortium on 24 December 2013

The previous human reference genome GRCh37 was the nineteenth version This build contained around 250 gaps, whereas the first version had roughly 150,000 gaps The GRCh38 assembly saw the closure or reduction of more than 100 gaps Nanopore sequencing has seen the closure of 12 gaps in the GRCh38 reference assembly through the use of ultra-long reads

Recent genome assemblies are as follows:

Release name Date of release Equivalent UCSC version
GRCh38 Dec 2013 hg38
GRCh37 Feb 2009 hg19
NCBI Build 361 Mar 2006 hg18
NCBI Build 35 May 2004 hg17
NCBI Build 34 Jul 2003 hg16

Mouse reference genome

Recent mouse genome assemblies are as follows:

Release name Date of release Equivalent UCSC version
GRCm38 Dec 2011 mm10
NCBI Build 37 Jul 2007 mm9
NCBI Build 36 Feb 2006 mm8
NCBI Build 35 Aug 2005 mm7
NCBI Build 34 Mar 2005 mm6

Tutorials

  • Reference Genome Sequencing: Conifer Genomics
  • Selective Sequencing Through Combinatorial Pooling

References

  1. ^ a b Editorial October 2010 "E pluribus unum" Nature Methods 7 5: 331 doi:101038/nmeth0510-331 PMC 415373  
  2. ^ a b Wade, Nicholas May 31, 2007 "Genome of DNA Pioneer Is Deciphered" New York Times Retrieved February 21, 2009 
  3. ^ Donors were recruited by advertisement in The Buffalo News, on Sunday, March 23, 1997 The first ten male and ten female volunteers were invited to make an appointment with the project's genetic counselors and donate blood from which DNA was extracted As a result of how the DNA samples were processed, about 80 percent of the reference genome came from eight people and one male, designated RP11, accounts for 66 percent of the total
  4. ^ Scherer, Stewart 2008 A short guide to the human genome CSHL Press p 135 ISBN 0-87969-791-1 
  5. ^ a b Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM 2008 "The complete genome of an individual by massively parallel DNA sequencing" Nature 452 7189: 872–6 Bibcode:2008Natur452872W doi:101038/nature06884 PMID 18421352 
  6. ^ The exception to this is J Craig Venter whose DNA was sequenced and assembled using shotgun sequencing methods
  7. ^ MHC Sequencing Consortium 1999 "Complete sequence and gene map of a human major histocompatibility complex" Nature 401 6756: 921–923 Bibcode:1999Natur401921T doi:101038/44853 PMID 10553908 
  8. ^ Logan DW, Marton TF, Stowers L 2008 Vosshall, Leslie B, ed "Species specificity in major urinary proteins by parallel evolution" PLoS ONE 3 9: e3280 Bibcode:2008PLoSO33280L doi:101371/journalpone0003280 PMC 2533699  PMID 18815613 CS1 maint: Multiple names: authors list link
  9. ^ Hurst J, Beynon RJ, Roberts SC, Wyatt TD October 2007 Urinary Lipocalins in Rodenta:is there a Generic Model Chemical Signals in Vertebrates 11 Springer New York ISBN 978-0-387-73944-1 
  10. ^ Flicek P, Aken BL, Beal K, et al January 2008 "Ensembl 2008" Nucleic Acids Res 36 Database issue: D707–14 doi:101093/nar/gkm988 PMC 2238821  PMID 18000006 
  11. ^ "Help - Glossary - Homo sapiens - Ensembl genome browser 87" wwwensemblorg 
  12. ^ "Golden path length | VectorBase" wwwvectorbaseorg Retrieved 2016-12-12 
  13. ^ "Help - Glossary - Homo sapiens - Ensembl genome browser 87" wwwensemblorg 
  14. ^ "Whole assembly vs Golden path length in Ensembl - SEQanswers" seqanswerscom Retrieved 2016-12-12 
  15. ^ New human genome assembly GRCh38 released, NCBI news
  16. ^ Jain, Miten; Koren, Sergey; Miga, Karen H; Quick, Josh; Rand, Arthur C; Sasani, Thomas A; Tyson, John R; Beggs, Andrew D; Dilthey, Alexander T 2018-01-29 "Nanopore sequencing and assembly of a human genome with ultra-long reads" Nature Biotechnology doi:101038/nbt4060 ISSN 1546-1696 
  17. ^ a b "UCSC Genome Bioinformatics: FAQ" genomeucscedu Retrieved 2016-08-18 

External links

  • Genome Reference Consortium

reference genome, reference genome algorithm, reference genome hg19, reference genome mm10, reference genome sequence, reference genomes


Reference genome Information about

Reference genome


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    Reference genome beatiful post thanks!

    29.10.2014


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