A Comparative Analysis of Software Engineering Approaches for Sequence Analysis

A Comparative Analysis of Software Engineering Approaches for Sequence Analysis

Muneer Ahmad (King Faisal University, Saudi Arabia), Low Tang Jung (University Technology PETRONAS, Malaysia) and Noor Zaman (King Faisal University, Saudi Arabia)
DOI: 10.4018/978-1-4666-4301-7.ch053
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Abstract

DNA is considered the building block of living species. DNA sequence alignment and analysis have been big challenges for the scientists for many years. This research presents a comparative analysis of state of the art software engineering approaches for sequence analysis, i.e. genome sequences in particular. Sequence analysis problems are NP hard and need optimal solutions. The underlying problems stated are duplicate sequence detection, sequence matching by relevance, and sequence analysis by approximate comparison in general and by using tools, i.e. Matlab and multi-lingual sequence analysis. The usefulness of these operations is also highlighted, and future expectations are described. The proposal describes the concepts, tools, methodologies, and algorithms being used for sequence analysis. The sequences contain the precious information that needs to be mined for useful purposes. There is high concentration required to model the optimal solution. The similarity and alignments concepts cannot be addressed directly with one technique or algorithm; a better performance is achieved by the comprehension of different concepts.
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A Brief Discussion Of Research Over Sequence Analysis

We have presented a brief summary of research done for sequence analysis, Bansal (1995) has presented a sophisticated way for the presentation of information in the form of a frame work which helps understanding multiple sequences as ADT (abstract tool to integrate information achieved from proposed idea). The authors tried to develop a library that could contain generic high level language for generation of useful phylo-genetic tree. Complex analysis at multiple sequences had been performed by derived groups of amino acids in homologous protein (sharing some common properties along with identification of constrained columns. A help from PROLOG TOOL was taken to apply proposed frame work.

Kappen and Salbaum (2003) had presented a sequence comparison approach that could annotate a comparison between a mouse chromosome 9 and a human chromosome 15, the data draft sequences had been obtained from genetic databases and a complex map containing 14 genes has been presented as a genome map, the framework described in the paper for data interpretation and demonstration can be quite helpful for generation of more complex maps provided time constrained is kept in mind, the ideas may lead towards implementation of automated genome annotation techniques. Another added benefit of this approach was the extraction of common properties between species.

Nahar, Hamel, Popstova and Gogarten (2007) had proposed an interactive tool which was web based and provided comparative genome sequence analysis. The authors have taken help from self adjusting maps for depiction of possible evolutionary concepts in to achieve certain results. The visual identification of horizontally transferred genes was not available in other techniques/tools.

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