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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]
There are two common methods in which to construct a DNA molecular-weight size marker. [3] One such method employs the technique of partial ligation. [3] DNA ligation is the process by which linear DNA pieces are connected to each other via covalent bonds; more specifically, these bonds are phosphodiester bonds. [4]
The level of unique gene expression is represented by the count of transcripts present per million molecules, similar to SAGE output. A significant advantage is the larger library size compared with SAGE. An MPSS library typically holds 1 million signature tags, which is roughly 20 times the size of a SAGE library.
1 to 16 million Around 24 hours $667 Low-cost of instrument ($10,000) Chain termination (Sanger sequencing) 400 to 900 bp: 99.9%: N/A: 20 minutes to 3 hours: $2,400,000: Useful for many applications. More expensive and impractical for larger sequencing projects. This method also requires the time-consuming step of plasmid cloning or PCR.
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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]
In B. subtilis the length of the transferred DNA is more than 1 million bases, is likely double stranded DNA, and is often more than a third of the total chromosome length of 4215 kb. [24] Approximately 7-9% of the recipient cells take up an entire chromosome. [25]