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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]
In 2012, with cameras operating at more than 10 MHz A/D conversion rates and available optics, fluidics and enzymatics, throughput can be multiples of 1 million nucleotides/second, corresponding roughly to 1 human genome equivalent at 1x coverage per hour per instrument, and 1 human genome re-sequenced (at approx. 30x) per day per instrument ...
The ISQ symbols for the bit and byte are bit and B, respectively.In the context of data-rate units, one byte consists of 8 bits, and is synonymous with the unit octet.The abbreviation bps is often used to mean bit/s, so that when a 1 Mbps connection is advertised, it usually means that the maximum achievable bandwidth is 1 Mbit/s (one million bits per second), which is 0.125 MB/s (megabyte per ...
2×10 3: UNIVAC I, first American commercially available electronic general-purpose stored program digital computer, 1951 [2] 3×10 3: PDP-1 commercial minicomputer, 1959 [2] 15×10 3: IBM Naval Ordnance Research Calculator, 1954; 24×10 3: AN/FSQ-7 Combat Direction Central, 1957 [2] 30×10 3: IBM 1130 commercial minicomputer, 1965 [2]
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.
Faster and efficient tools are needed to keep pace with the high-throughput sequencing, because the BLAST-based approaches such as MG-RAST or MEGAN run slowly to annotate large samples (e.g., several hours to process a small/medium size dataset/sample [56]). Thus, ultra-fast classifiers have recently emerged, thanks to more affordable powerful ...