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Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Perhaps the most important use of Phred quality scores is the automatic determination of accurate, quality-based consensus sequences .
Microfluidic Sanger sequencing is a lab-on-a-chip application for DNA sequencing, in which the Sanger sequencing steps (thermal cycling, sample purification, and capillary electrophoresis) are integrated on a wafer-scale chip using nanoliter-scale sample volumes. This technology generates long and accurate sequence reads, while obviating many ...
This format matched the different sequencing chemistry used by SOLiD sequencers. Initial representations only used nucleotide bases at the start of the sequence, but later versions included bases embedded at periodic intervals to improve basecalling and mapping accuracy. The quality values for CSFASTQ are identical to those of the Sanger format.
Quality control assesses the quality of sequencing reads obtained from the sequencing technology (e.g. Illumina). It is the first step in sequence analysis to limit wrong conclusions due to poor quality data. The tools used at this stage depend on the sequencing platform.
An electropherogram (also called electrophoretogram, sequencing chromatogram, EPG, and e-gram) is a record or chart produced when electrophoresis is used in an analytical technique, primarily in the fields of forensic biology, molecular biology, and biochemistry. [1]
SOLiD applies sequencing by ligation and dual base encoding. The first SOLiD system was launched in 2007, generating reading lengths of 35bp and 3G data per run. After five upgrades, the 5500xl sequencing system was released in 2010, considerably increasing read length to 85bp, improving accuracy up to 99.99% and producing 30G per 7-day run. [10]
[1] [2] Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. [3] Physical coverage, the cumulative length of reads or read pairs expressed as a multiple of genome size. [4] Genomic coverage, the percentage of all base pairs or loci of the genome covered by sequencing.
In contrast to directed sequencing, shotgun sequencing of DNA is a more rapid sequencing strategy. [6] There is a technique from the "old time" of genome sequencing. The underlying method for sequencing is the Sanger chain termination method which can have read lengths between 100 and 1000 basepairs (depending on the instruments used).
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