JAligner The Smith-Waterman algorithm implemented in Java for biological local pairwise sequence alignment
Download

JAligner Ranking & Summary

JAligner Tags

sequence align aligner sequence aligner align sequence sequence alignment

JAligner Description

The Smith-Waterman algorithm implemented in Java for biological local pairwise sequence alignment 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. Here are some key features of "JAligner": · The space complexity to perform the dynamic programming with the main similarity scores matrix and the 2 auxiliary gaps matrices is reduced from O(m?n) to O(n), where m and n are the sizes of the vertical sequence and horizontal sequence respectively, by using sufficient single-dimensional arrays of size n instead of the original two-dimensional arrays of size m?n. · The two-dimensional array of size m?n, for holding the traceback directions (diagonal, left, up and stop), is mapped into a single-dimensional array of size m?n. This approach speeds up the process of memory allocation because the Java Virtual Machine (JVM) attempts to allocate a single-dimensional array of m?n "bytes" (primitive data type), instead of attempting to allocate an array of m "objects", each of which is an "array" of n bytes. · In addition to the already included 70 scoring matrices, which have been picked up from the NCBI site, JAligner will also work with user-defined scoring matrices. · It is easy to use JAligner through a friendly Graphical User Interface (GUI), simple command line syntax or reusable Programming Application Interface (API).

JAligner Related Software