Sequence Accuracy and Verification

Stephan Beck, The Sanger Centre, Cambridge, UK

Published online: September 2005

DOI: 10.1038/npg.els.0005390

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 base-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 1.
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 References
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 Web Links
    ePath Ensembl Trace Server http://trace.ensembl.org/
    ePath Genome Sequencing Center. International Finishing Standards for the Human Genome Project (Version September 7, 2001) http://genome.wustl.edu/gsc/Overview/finrules/hgfinrules.html
    ePath National Human Genome Research Institute (NHGRI). NHGRI Standard for Quality of Human Genomic Sequence http://www.nhgri.nih.gov:80/Grant_info/Funding/Statements/RFA/quality_standard.html
    ePath National Center for Biotechnology Information: NCBI News http://www.ncbi.nlm.nih.gov/Web/Newsltr/feb98.html#GenBank
    ePath Project Ensembl. Ensembl Genome Browser http://www.ensembl.org/
    ePath 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 http://www.gene.ucl.ac.uk/hugo/bermuda2.htm
    ePath The Phred/Phrap/Consed System home page http://www.phrap.org
    ePath The Wellcome Trust Sanger Institute Human Blast Server http://www.sanger.ac.uk/HGP/blast_server.shtml
    ePath The Wellcome Trust Sanger Institute: software http://www.sanger.ac.uk/Software/
    ePath UCSC Human Genome Project Working Draft http://genome.ucsc.edu/

Related Sub-Topics:

Nucleic Acid Structure | Bioinformatics | Gene and Genome Structure and Organisation | Techniques and Tools in Clinical Genetics | Statistical Methodology in Genetics | DNA Structure and Function | Techniques and Tools in Molecular Biology
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Article Title: Sequence Accuracy and Verification
 
How to Cite close
Beck, Stephan(Sep 2005) Sequence Accuracy and Verification. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005390]