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This is an example of a scaffold. Scaffolding is a technique used in bioinformatics. It is defined as follows: [1] Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically contiguous sequences corresponding to read overlaps.
N50 statistic defines assembly quality in terms of contiguity. Given a set of contigs, the N50 is defined as the sequence length of the shortest contig at 50% of the total assembly length. It can be thought of as the point of half of the mass of the distribution; the number of bases from all contigs longer than the N50 will be close to the ...
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.
However, such measures do not assess assembly completeness in terms of gene content. Some tools evaluate the quality of an assembly after the fact. For instance, BUSCO (Benchmarking Universal Single-Copy Orthologs) is a measure of gene completeness in a genome, gene set, or transcriptome , using the fact that many genes are present only as ...
For the snake genome assembly, the Wellcome Trust Sanger Institute using SGA, performed best. For all assemblies, SGA, BCM, Meraculous, and Ray submitted competitive assemblies and evaluations. The results of the many assemblies and evaluations described here suggest that while one assembler may perform well on one species, it may not perform ...
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.
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]
This particular function is considered a scaffold's most basic function. Scaffolds assemble signaling components of a cascade into complexes. This assembly may be able to enhance signaling specificity by preventing unnecessary interactions between signaling proteins, and enhance signaling efficiency by increasing the proximity and effective concentration of components in the scaffold complex.