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Gene length: Longer genes will have more fragments/reads/counts than shorter genes if transcript expression is the same. This is adjusted by dividing the FPM by the length of a feature (which can be a gene, transcript, or exon), resulting in the metric fragments per kilobase of feature per million mapped reads (FPKM). [90]
Sequencing technologies vary in the length of reads produced. Reads of length 20-40 base pairs (bp) are referred to as ultra-short. [2] Typical sequencers produce read lengths in the range of 100-500 bp. [3] However, Pacific Biosciences platforms produce read lengths of approximately 1500 bp. [4] Read length is a factor which can affect the results of biological studies. [5]
The size of restriction fragments determines the resolution of interaction mapping. Restriction enzymes (REs) that make cuts on 6bp recognition sequences, such as EcoR1 or HindIII, are used for this purpose, as they cut the genome once every 4000bp, giving ~ 1 million fragments in the human genome.
To obtain a high complexity library of ligation products that will ensure high resolution and depth of data, a sample of 20–25 million cells is required as input for Hi-C. [3] [4] Primary human samples, which may be available only in fewer cell numbers, could be used for standard Hi-C library preparation with as low as 1–5 million cells. [4]
A molecular marker is then generated when specific fragments are selected for amplification. AFLP markers are run alongside a DNA marker on a gel. A common AFLP DNA marker is 30-330bp long. [32] The fragments of this marker lie at 10bp intervals to increase precision. RAPD Random amplified polymorphic DNA is a technique that is conducted ...
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]
DNA Nanoball Sequencing involves isolating DNA that is to be sequenced, shearing it into small 100 – 350 base pair (bp) fragments, ligating adapter sequences to the fragments, and circularizing the fragments. The circular fragments are copied by rolling circle replication resulting in many single-stranded copies of each fragment. The DNA ...
The entire set of fragments must be cloned together with the vector, and separation of clones can occur after. In either case, the fragments are ligated into a vector that has been digested with the same restriction enzyme. The vector containing the inserted fragments of genomic DNA can then be introduced into a host organism. [1]