Contig

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Overlapping sequences from PET-DNA sequencing.

A contig (. Engl of contiguous = adjacent, contiguous) is a set of overlapping DNA - or protein -pieces ( reads ) that originate from the same genetic source. Such a contig can be used to derive the original DNA sequence of this genetic source (e.g. the sequence of a chromosome ).

A contig card shows the relative order of a related contig library. B. represent a complete chromosome .

Sequencing

In DNA sequencing and especially in shotgun sequencing , the DNA sequence or in de novo peptide sequencing the amino acid sequence has to be determined by stringing together the various contigs. For genome sequencing, the genomic DNA is often fragmented in preparation and the fragments then copied. The individual DNA strands then have different, partially overlapping sequences which, when lined up, result in the complete sequence.

A contig arises under the assumption that the associated reads are correct. However, there are weaknesses in all sequencing methods used so far, which are often also known and whose influence the manufacturers try to minimize. A contig can also consist of a single read, but every overlapping read (ideally from different directions or even by a different sequencing method) increases the probability that reality can be seen here.

Individual evidence

  1. ↑ A. Guthals, KR Clauser, N. Bandeira: Shotgun protein sequencing with meta-contig assembly. In: Molecular & cellular proteomics: MCP. Volume 11, number 10, October 2012, ISSN  1535-9484 , pp. 1084-1096, doi : 10.1074 / mcp.M111.015768 , PMID 22798278 , PMC 3494147 (free full text).
  2. ^ Rodger Staden: A strategy of DNA sequencing employing computer programs . In: Nucleic Acids Research . 7, 1979, pp. 2601-2610. PMC 327874 (free full text).
  3. ↑ SH Lin, YC Liao: CISA: contig integrator for sequence assembly of bacterial genomes. In: PloS one. Volume 8, number 3, 2013, ISSN  1932-6203 , p. E60843, doi : 10.1371 / journal.pone.0060843 , PMID 23556006 , PMC 3610655 (free full text).
  4. ↑ Z. Frenkel, E. Paux, D. Mester, C. Feuillet, A. Korol: LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes. In: BMC Bioinformatics. Volume 11, 2010, ISSN  1471-2105 , p. 584, doi : 10.1186 / 1471-2105-11-584 , PMID 21118513 , PMC 3098104 (free full text).