Solving Sequence Alignment Problem using Pipeline Approach

This paper presents two models based on pipeline approach for determining pair-wise sequence alignment of two molecular sequences. One of the models considers a variation of Needleman-Wunsch method as a basic algorithm and other is based on the use of scoring matrix for alignment. The basic purpose of using the pipelines is to reduce the time-complexity of alignment significantly. Paper also discusses the design & implementation of the basic linear version of the algorithms in our software tool by the name "Sequence Comparison and Analysis Tool (SCAT)". Our tool also provides the option of sequence alignment on the basis of common grouping like chemical, functional & structural etc. The software tool is implemented using Visual Basic-6 package with user-friendly windows environment.

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