Sage-Tips

How does contig assembly work?

The assembly of a contig map involves several steps. First, DNA is sheared into larger (50–200kb) pieces, which are cloned into BACs or PACs to form a BAC 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.

What is contig how are they created?

A contig is the physical map, which results from putting together several little overlapping bits of DNA into a longer sequence. The contig is the physical map resulting from taking small pieces of DNA that overlap and putting them together into a longer sequence.

What technique is chromosome walking?

Primer walking, also called “Chromosome walking” is a technique used to clone a gene (e.g., disease gene) from its known closest markers (e.g., known gene). As a result, it is employed in cloning and sequencing efforts in plants, fungi, and mammals with minor alterations.

What is the difference between scaffold and contig?

A scaffold is a portion of the genome sequence reconstructed from end-sequenced whole-genome shotgun clones. A contig is a contiguous length of genomic sequence in which the order of bases is known to a high confidence level.

How are scaffolds assembled?

Scaffolds are created by chaining contigs together using additional information about the relative position and orientation of the contigs in the genome. Scaffolding is often used for short-read assemblies to make sense of the fragmented genome assemblies containing short contigs.

What is clone contig method?

a method to obtain the sequence of a GENOME involving the construction of a clone CONTIG map and sequencing the set of contiguous clones individually, by the shot-gun method. Such an approach is often used to sequence EUKARYOTIC genomes, see HUMAN GENOME PROJECT. …

What is the difference between a contig and a scaffold?

What are limitations of chromosome walking?

This was the first method, called chromosome walking. But there is a limitation to the speed of chromosome walking and that is because of the small size of the fragments that are to be cloned, another limitation is the difficulty of walking through the repeated sequence that are scattered through the gene.

What are chromosome banding techniques?

Chromosome banding techniques produce a series of consistent landmarks along the length of metaphase chromosomes that allow for both recognition of individual chromosomes within a genome and identification of specific segments of individual chromosomes.

How does the chromosome get painted with different colors?

The simultaneous hybridization of multiple chromosome painting probes, each tagged with a specific fluorochrome or fluorochrome combination, has resulted in the differential color display of human (and mouse) chromosomes, i.e. color karyotyping.

What is chromosome walking?

• In chromosome walking, one begins with a DNA fragment that contains a known gene/genetic marker, e.g., an RFLP marker. •The sequence located at one end of this fragment is used to identify a clone that has such a DNA insert, which partly overlaps the first segment.

What is Chromosome jumping?

Chromosome Jumping •The techniques of chromosome jumping and chromosome walking are used for the construction of restriction maps of genomes. •Chromosome jumping is used for rather large DNA fragments, usually of several hundred kb in size, while chromosome walking is applicable to much smaller DNA fragments.

Can a contig of BACs cover the entire chromosome?

Since these clones should cover the entire genome/chromosome, it is theoretically possible to assemble a contig of BACs that covers the entire chromosome. 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.

What is a contig in genome sequencing?

In bottom-up sequencing projects, a contig refers to overlapping sequence data ( reads ); in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is used to guide sequencing and assembly.