FANDOM


A contig is a collection of clones, which are large pieces of DNA that are cloned into vectors (1). These configs are used in genomics because they enable the DNA to be sequenced and this help to determine the funtion and the structure of a genome. The order of the vectors is identified by overlapping regions of the DNA within each contig (1). This collection of clones is a map of the chromosome (1).


Contig

This figure shows how fragments of DNA can used to from a config. Photo courtesy of: http://gcat.davidson.edu/phast/












Construction of a ContigEdit

Bacterial Artificial Chromosomes (BAC) are constructed by using the bacterial F factor of E. coli (1). The BAC is a vector that can be purified into DNA, and produce DNA that is very stable (2). When the DNA is cloned and separated using BAC's there are overlapping regions within each of the BAC contigs (1). Genetic markers can be used to align the BAC contigs (1). For example if two genes on a chromosome are known and there are multiple BAC contigs they can be aligned by starting with the contigs that resemble the known genes (1). After starting with the known contigs the next contig in the correct sequence can be identified because it will overlap with the contig that contains the known gene sequence (1). The chromosome can be further built from there to create a physical map of the original chromosome (1). This can be seen in the figure below. This link for this photo connects to a pdf.

Contig

This shows 7 configs that represent a physical map of chromosome 11. http://www.qcc.cuny.edu/pv_obj_cache/pv_obj_id_699FAFC67B09C07ADE05D013057398349C8C1900/filename/chapt20_Structural%20Genomics.pdf

220px-DNA Sequencing gDNA libraries

Amplification of DNA using Configs.











The amount of overlap between the contigs can be estimated using STS markers, restriction enzymes, and southern blotting (1). If there are a large number of similar STS markers there is also a large degree of overlap between each of the contigs (3). Restriction enzymes can also be used to estimate that amount of overlap between the contigs because if the two contigs overlap they will have similar restriction enzymes (3). If there are a small number of STS and restriction sites, or if regions of DNA were unstable during the cloning then there could be a large number of gaps when the contig is being constructed (3). To remedy gaps the sequence at the end of the contig can be used to close them (3).

Contigs and ScienceEdit

Contigs can be used in science to evaluate different regions in DNA that could be closely related. One study by NijKamp J.F. et al. used contig graphs and an algorithm called MaryGold to detect bubble structures within the contigs. The bubbles within the contigs were genomic regions that were very closly related in a metagenomic samples (4).


ReferencesEdit

(1). Brooker, R. J. (2012). Genetics: Analysis & Principles. USA: McGraw-Hill

(2). Construction of a BAC Contig Map of Chromosome 16q by Two-Dimensional Overgo Hybridization (2000). Link:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310869/

(3). Wikipedia Contig (2013). Link: http://en.wikipedia.org/wiki/Contig

4. Nijkamp, J. F. et al., Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. (2013) Link: http://www.ncbi.nlm.nih.gov/pubmed/24058058