Difference Between Contig and Scaffold

A scaffold is a portion of the genome sequence reconstructed from end-sequenced whole-genome shotgun clones. Scaffolds are composed of contigs and gaps. A contig is a contiguous length of genomic sequence in which the order of bases is known to a high confidence level. ... In some cases, scaffolds can overlap.

1. What is a contig in sequencing?
2. What is DNA scaffold?
3. What is clone contig?
4. How is a contig generated?
5. How many genes are there in contig 1?
6. What is contig length?
7. What does scaffold mean?
8. What is chromosome scaffold?
9. What is a cell scaffold?
10. What is clone by clone sequencing?
11. How many ddNTPs are used in sequencing?
12. What is a sequence read?

What is a contig in sequencing?

A contig--from the word "contiguous"--is a series of overlapping DNA sequences used to make a physical map that reconstructs the original DNA sequence of a chromosome or a region of a chromosome. A contig can also refer to one of the DNA sequences used in making such a map.

What is DNA scaffold?

Scaffold: 1. In genetics, the chromosome structure consisting entirely of nonhistone proteins remaining after all the DNA and histone proteins have been removed from a chromosome. 2. In genomic mapping, a series of contigs that are in the right order but not necessarily connected in one continuous stretch of sequence.

What is clone contig?

The clone contig approach is the conventional method for obtaining the sequence of a eukaryotic genome and has also been used with those microbial genomes that have previously been mapped by genetic and/or physical means.

How is a contig generated?

Kmers are produced from the reads that overlap the gap and are used to eat into the gap from each end using kmers that overlap the end of the contig by k-1. The process is iterated until the gap is filled, or no more overlaps can be found.

How many genes are there in contig 1?

There are six features (genes) in contig 1.

What is contig length?

Here, a contig still refers to any contiguous stretch of sequence data created by read overlap. Because the fragments are of known length, the distance between the two end reads from each fragment is known.

What does scaffold mean?

1a : a temporary or movable platform for workers (such as bricklayers, painters, or miners) to stand or sit on when working at a height above the floor or ground. b : a platform on which a criminal is executed (as by hanging or beheading) c : a platform at a height above ground or floor level.

What is chromosome scaffold?

Chromosome scaffold represents a continuous protein substructure revealed in isolated metaphase chromosomes after harsh extraction. According to postulates of the widespread radial loop model the scaffold plays an important role in the formation and maintenance of structural integrity of the mitotic chromosomes.

What is a cell scaffold?

Scaffolds are materials that have been engineered to cause desirable cellular interactions to contribute to the formation of new functional tissues for medical purposes. Cells are often 'seeded' into these structures capable of supporting three-dimensional tissue formation.

What is clone by clone sequencing?

During clone-by-clone sequencing, a map of each chromosome of the genome is made before the DNA is split up into fragments ready for sequencing. ... The DNA fragments are then sequenced, starting with the known sequence of the vector and extending out into the unknown sequence of the DNA.

How many ddNTPs are used in sequencing?

The four reactions include normal A, G, C, and T deoxynucleotide triphosphates (dNTPs), and each contains a low level of one of four dideoxynucleotide triphosphates (ddNTPs): ddATP, ddGTP, ddCTP, or ddTTP. The four reactions can be named A, G, C and T, according to which of the four ddNTPs was included.

What is a sequence read?

In DNA sequencing, a read is an inferred sequence of base pairs (or base pair probabilities) corresponding to all or part of a single DNA fragment. A typical sequencing experiment involves fragmentation of the genome into millions of molecules, which are size-selected and ligated to adapters.