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When creating a draft genome, individual reads of DNA are second assembled into contigs, which, by the nature of their assembly, have gaps between them. The next step is to then bridge the gaps between these contigs to create a scaffold. [2] This can be done using either optical mapping or mate-pair sequencing. [3]
The contig lengths of assembly B are the same as those of assembly A, except for the presence of two additional contigs with lengths of 10 kbp and 5 kbp. The size of assembly B is 305 kbp, the N50 contig length drops to 50 kbp because 80 + 70 + 50 is greater than 50% of 305, and the L50 contig count is 3 contigs.
Genome assembly is normally done by one of two methods: assembly using a reference genome as a scaffold, [11] or de novo [12] assembly. The scaffolding approach can be useful if the genome of a similar organism has been previously sequenced. This process involves assembling the genome of interest by comparing it to a known genome or scaffold.
The smaller the number of scaffolds per chromosome, until a single scaffold occupies an entire chromosome, the greater the continuity of the genome assembly. [11] [12] [13] Other related parameters are N50 and L50. N50 is the length of the contigs/scaffolds in which the 50% of the assembly is found in fragments of this length or greater, while ...
A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA. [1] In bottom-up sequencing projects, a contig refers to overlapping sequence data (); [2] 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. [3]
In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. [1] This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. [1]
It has been known for many years that a polymer meshwork, a so-called "nuclear matrix" or "nuclear-scaffold" is an essential component of eukaryotic nuclei. This nuclear skeleton acts as a dynamic support for many specialized events concerning the readout a spread of genetic information (see below). S/MARs map to non-random locations in the genome.
Coverage of genome by assembly: for this metric, BGI's assembly via SOAPdenovo performed best, with 98.8% of the total genome being covered. All assemblers performed relatively well in this category, with all but three groups having coverage of 90% and higher, and the lowest total coverage being 78.5% (Dept. of Comp. Sci., University of Chicago ...