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PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools Cross-platform: GPL v2 Open Bioinformatics Foundation: Biopython: Python language toolkit Cross-platform: Biopython [2] Open Bioinformatics Foundation: BioRuby: Ruby language toolkit Linux, macOS, Windows [3] GPL ...
Both + Ends-free: P. Aboyoun: 2008 BioPerl dpAlign Dynamic programming: Both: Both + Ends-free: Y. M. Chan: 2003 BLASTZ, LASTZ Seeded pattern-matching: Nucleotide: Local: Schwartz et al. [18] [19] 2004,2009 CUDAlign DNA sequence alignment of unrestricted size in single or multiple GPUs Nucleotide: Local, SemiGlobal, Global: E. Sandes [20] [21 ...
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
The higher the score of the shuffled sequences the less significant the matches found between original database and query sequence. [5] The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
The method plots data points that represent a specific time and fluorescence intensity at various wavelengths of light to represent a DNA profile. [ 2 ] [ page needed ] In the field of genetics, an electropherogram is a plot of DNA fragment sizes, typically used for genotyping such as DNA sequencing . [ 3 ]
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
Alignment-free methods can broadly be classified into five categories: a) methods based on k-mer/word frequency, b) methods based on the length of common substrings, c) methods based on the number of (spaced) word matches, d) methods based on micro-alignments, e) methods based on information theory and f) methods based on graphical representation.
The component programs of phylip use several different formats, all of which are relatively simple. Programs for the analysis of DNA sequence alignments, protein sequence alignments, or discrete characters (e.g., morphological data) can accept those data in sequential or interleaved format, as shown below. Sequential format: