JAligner

	JAligner JAligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvementGotoh O (1982). An improved algorithm for matching biological sequences. ''J Mol Biol, 162:705-708''. for biological local pairwise sequence alignment using the affine gap penalty model. It was written by Ahmed Moustafa. See also * Sequence alignment software * Clustal Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its ... References External links Official website {{bioinformatics-stub Phylogenetics software ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu]
	Sequence Alignment Software This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins. Database search only Sequence type: protein or nucleotide Pairwise alignment Sequence type: protein or nucleotide *Alignment type: local or global Multiple sequence alignment Sequence type: protein or nucleotide. *Alignment type: local or global Genomics analysis Sequence type: protein or nucleotide Motif finding Sequence type: protein or nucleotide Benchmarking Alignment viewers, editors Please see List of alignment visualization software. Short-read sequence alignment See also List of open source bioinformatics software References {{Reflist Sequence Sequence alignment software This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu]
picture info	Clustal Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its algorithm are also detailed in their respective categories. Available operating systems listed in the sidebar are a combination of the software availability and may not be supported for every current version of the Clustal tools. Clustal Omega has the widest variety of operating systems out of all the Clustal tools. History There have been many variations of the Clustal software, all of which are listed below: * Clustal: The original software for multiple sequence alignments, created by Des Higgins in 1988, was based on deriving phylogenetic trees from pairwise sequences of amino acids or nucleotides. * ClustalV: The second generation of the Clustal software was released in 1992 and was a rewrite of the original Clustal package. It int ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu]
picture info	Java (programming Language) Java is a high-level, class-based, object-oriented programming language that is designed to have as few implementation dependencies as possible. It is a general-purpose programming language intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. , Java was one of the most popular programming languages in use according to GitHub, particularly for client–server web applications, with a reported 9 million developers. Java was originally develo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu]
picture info	Sequence Alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between amino acids occupying a p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu]
picture info	Gap Penalty A Gap penalty is a method of scoring alignments of two or more sequences. When aligning sequences, introducing gaps in the sequences can allow an alignment algorithm to match more terms than a gap-less alignment can. However, minimizing gaps in an alignment is important to create a useful alignment. Too many gaps can cause an alignment to become meaningless. Gap penalties are used to adjust alignment scores based on the number and length of gaps. The five main types of gap penalties are constant, linear, affine, convex, and profile-based. Applications * Genetic sequence alignment - In bioinformatics, gaps are used to account for genetic mutations occurring from insertions or deletions in the sequence, sometimes referred to as ''indels''. Insertions or deletions can occur due to single mutations, unbalanced crossover in meiosis, slipped strand mispairing, and chromosomal translocation. The notion of a gap in an alignment is important in many biological applications, since the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu]