Editing Contig (section)

==BAC contigs==
Contig can also refer to the overlapping [[Bacterial artificial chromosome|clones]] that form a [[Gene mapping#Physical Mapping|physical map]] of a chromosome when the '''top-down''' or '''[[Shotgun sequencing#Hierarchical Shotgun sequencing|hierarchical]]''' sequencing strategy is used.<ref name="contig assembly" />  In this sequencing method, a low-resolution [[Gene mapping#Physical Mapping|map]] is made prior to sequencing in order to provide a framework to guide the later assembly of the sequence reads of the genome. This map identifies the relative positions and overlap of the clones used for sequencing.  Sets of overlapping clones that form a contiguous stretch of DNA are called contigs; the minimum number of clones that form a contig that covers the entire chromosome comprise the tiling path that is used for sequencing. Once a tiling path has been selected, its component BACs are sheared into smaller fragments and sequenced. Contigs therefore provide the framework for hierarchical sequencing.<ref name="genome map" />

The assembly of a contig map involves several steps.  First, DNA is sheared into larger (50–200kb) pieces, which are cloned into [[Bacterial Artificial Chromosome|BACs]] or [[P1-derived artificial chromosome|PACs]] to form a BAC [[Library (biology)|library]].  Since these clones should cover the entire genome/chromosome, it is theoretically possible to assemble a contig of BACs that covers the entire chromosome.<ref name="contig assembly" /> Reality, however, is not always ideal. Gaps often remain, and a scaffold—consisting of contigs and gaps—that covers the map region is often the first result.<ref name="contig assembly" /> The gaps between contigs can be closed by various methods outlined below.

===Construction of BAC contigs===
BAC contigs are constructed by aligning BAC regions of known overlap via a variety of methods. One common strategy is to use [[sequence-tagged site]] (STS) content mapping to detect unique DNA sites in common between BACs.  The degree of overlap is roughly estimated by the number of STS markers in common between two clones, with more markers in common signifying a greater overlap.<ref name="textbook" /> Because this strategy provides only a very rough estimate of overlap, [[restriction digest]] fragment analysis, which provides a more precise measurement of clone overlap, is often used.<ref name="textbook" />  In this strategy, clones are treated with one or two [[restriction enzyme]]s and the resulting fragments separated by [[gel electrophoresis]].  If two clones, they will likely have restriction sites in common, and will thus share several fragments.<ref name="genome map" />  Because the number of fragments in common and the length of these fragments is known (the length is judged by comparison to a size standard), the degree of overlap can be deduced to a high degree of precision.

===Gaps between contigs===
Gaps often remain after initial BAC contig construction.  These gaps occur if the [[Bacterial Artificial Chromosome]] (BAC) library screened has low complexity, meaning it does not contain a high number of STS or restriction sites, or if certain regions were less stable in cloning hosts and thus underrepresented in the library.<ref name="contig assembly" />  If gaps between contigs remain after STS landmark mapping and restriction fingerprinting have been performed, the sequencing of contig ends can be used to close these gaps.  This end-sequencing strategy essentially creates a novel STS with which to screen the other contigs.  Alternatively, the end sequence of a contig can be used as a primer to [[Primer walking|primer walk]] across the gap.<ref name="textbook" />