Sequence Accuracy and Verification


Analyses involving deoxyribonucleic acid sequences have to consider three main parameters concerning accuracy: sequence quality, sequence contiguity and sequence fidelity. Here, sequence quality defines the probability of error for any baseā€call, contiguity defines the completeness and correctness of the assembly of subsequences and fidelity defines the correctness of the genomic representation of the assembly.

Keywords: DNA sequence; assembly; contiguity; fidelity; quality

Figure 1.

The PHRAP quality scores of a typical human genome ‘draft’ sequence as available from the EMBL database.

Figure 2.

Levels of sequence contiguity. (N)100 indicates sequence gap in the clone assembly, (N)50000 indicates a bridged sequence gap in the chromosome assembly and (N)100000 indicates an unbridged sequence gap in the chromosome assembly. S indicates switch points between clone sequences in the chromosome assembly. Switch points are chosen arbitrarily within the middle sections of overlapping clone sequences.

Figure 3.

EMBL/GENBANK/DDBJ database entry for the draft sequence shown in Figure .



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Further Reading

Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.

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

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

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

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

Mullikin JC, Hunt SE, Cole CG, et al. (2000) An SNP map of human chromosome 22. Nature 407: 516–520.

Osoegawa K, Mammoser AG, Wu C, et al. (2001) A bacterial artificial chromosome library for sequencing the complete human genome. Genome Research 11: 483–496.

International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.

Web Links

Ensembl Trace Server

Genome Sequencing Center. International Finishing Standards for the Human Genome Project (Version September 7, 2001)

National Human Genome Research Institute (NHGRI). NHGRI Standard for Quality of Human Genomic Sequence

National Center for Biotechnology Information: NCBI News

Project Ensembl. Ensembl Genome Browser

Summary of the Report of the Second International Strategy Meeting on Human Genome Sequencing Bermuda, 27th February–2nd March 1997 sponsored by the Wellcome Trust

The Phred/Phrap/Consed System home page

The Wellcome Trust Sanger Institute Human Blast Server

The Wellcome Trust Sanger Institute: software

UCSC Human Genome Project Working Draft

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How to Cite close
Beck, Stephan(Sep 2005) Sequence Accuracy and Verification. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0005390]