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These algorithms typically do not work well for larger read sets, as they do not easily reach a global optimum in the assembly, and do not perform well on read sets that contain repeat regions. [1] Early de novo sequence assemblers, such as SEQAID [ 2 ] (1984) and CAP [ 3 ] (1992), used greedy algorithms, such as overlap-layout-consensus (OLC ...
For example, the algorithm QualComp [9] performs lossy compression with a rate (number of bits per quality value) specified by the user. Based on rate-distortion theory results, it allocates the number of bits so as to minimize the MSE (mean squared error) between the original (uncompressed) and the reconstructed (after compression) quality values.
Like strict phylip format files, relaxed phylip format files can be in interleaved format and include spaces and endlines within the sequence data. The programs that use distance data, like the neighbor program that implements the neighbor-joining method, also use a simple distance matrix format the includes only the number of taxa, their names ...
Phrap was routinely used in some of the largest sequencing projects in the Human Genome Sequencing Project and is currently one of the most widely used DNA sequence assembly programs in the biotech industry. Phrap uses Phred quality scores to determine highly accurate consensus sequences and to estimate the quality of the consensus sequences.
Consensus statements differ from medical guidelines, another form of state-of-the-science public statements. According to the NIH, "Consensus statements synthesize new information, largely from recent or ongoing medical research, that has implications for reevaluation of routine medical practices. They do not give specific algorithms or ...
In bioinformatics, MAFFT (multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. . Published in 2002, the first version used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the fast Fourier transfo
Distributed Evolutionary Algorithms in Python (DEAP) is an evolutionary computation framework for rapid prototyping and testing of ideas. [2] [3] [4] It incorporates the data structures and tools required to implement most common evolutionary computation techniques such as genetic algorithm, genetic programming, evolution strategies, particle swarm optimization, differential evolution, traffic ...
Thrombocytopenia – a deficiency of platelets; Pancytopenia – when all three types of blood cells; red blood cells, white blood cells, and platelets, are all deficient. This is a life-threatening disorder that is a characteristic of aplastic anemia. [3] There are also two general causes of cytopenia: autoimmune and refractory.