JAligner
Encyclopedia
JAligner is an open source Java
implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment
using the affine gap penalty
model. It was written by Ahmed Moustafa.
Java (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...
implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment
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...
using the affine gap penalty
Gap penalty
Gap penalties are used during sequence alignment. Gap penalties contribute to the overall score of alignments, and therefore, the size of the gap penalty relative to the entries in the similarity matrix affects the alignment that is finally selected...
model. It was written by Ahmed Moustafa.