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The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
RNA-Seq Atlas a reference database for gene expression profiling in normal tissue by next-generation sequencing. SRA The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores ...
Simulation of protein sequences along phylogenies under empirical and structurally constrained substitution models of protein evolution Simulating sequences forward in time, substitution models M. Arenas, H.G. Dos Santos, D. Posada, U. Bastolla ProteinEvolverABC [40] Coestimation of recombination and substitution rates in protein sequences
In bioinformatics and proteomics, ProbCons is an open source software for probabilistic consistency-based multiple alignment of amino acid sequences. It is one of the most efficient protein multiple sequence alignment programs, since it has repeatedly demonstrated a statistically significant advantage in accuracy over similar tools, including Clustal and MAFFT.
The new machine, called the IBM Selective Sequence Electronic Calculator (SSEC), was ready to be installed by August 1947. [9] Watson called such machines calculators because computer then referred to humans employed to perform calculations and he wanted to convey the message that IBM's machines were not designed to replace people. Rather they ...
Recently, sequence context-specific amino acid similarities have been derived that do not need substitution matrices but that rely on a library of sequence contexts instead. Using this idea, a context-specific extension of the popular BLAST program has been demonstrated to achieve a twofold sensitivity improvement for remotely related sequences ...
The BLOSUM62 matrix, the amino acids have been grouped and coloured based on Margaret Dayhoff's classification scheme. Positive and zero values have been highlighted. In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins.
The sequence produced by other choices of c can be written as a simple function of the sequence when c=1. [1]: 11 Specifically, if Y is the prototypical sequence defined by Y 0 = 0 and Y n+1 = aY n + 1 mod m, then a general sequence X n+1 = aX n + c mod m can be written as an affine function of Y: