DNA sequence comparison based on Tabular Representation
Journal Title: INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY - Year 2013, Vol 4, Issue 1
Abstract
DNA sequence comparison remains as one of the critical steps in the analysis of phylogenetic relationships between species. In order to get quantitative comparison, we want to devise an algorithm that would use the tabular representation of DNA sequences. The tabular approach of representation captures the essence of the base composition and distribution of the sequence. In this contribution, we take the tabular notation for DNA sequences and then these tables are compared to find the similarity/dissimilarity measure of the sequences. We have developed algorithms for comparing DNA sequences. These programs help us to search similar segments of sequences, calculate similarity scores and identify repetitions based on local sequence similarity. There are two approaches: one is to find the exact similarity and another is to find the measurement for similarity. The first approach is more sensitive, which can be used to search DNA sequence similarities only if complete matches occurred and can compare exactly similar sequences only. This approach violates if a single mismatch for any base character appears so it is not a general solution. To find the miss matches along with the matches we have suggested another approach which compiles the information matrix based on matches and miss matches. This approach is quiet general in terms of sequences which have a large fragment common with less no of dissimilar base characters. This alternate approach includes an additional step in the calculation of the similarity score that denotes multiple regions of similarity between sequences. For both these approaches computer programs are prepared and tested on data sets. These programs can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. In addition, these programs have been generalized to allow comparison of DNA sequences based on a variety of alternative scoring matrices. We have been developing tools for the analysis of protein The method is very simple and fast, and it can be used to analyze both short and long DNA sequences. The utility of this method is tested on the several sequences of species and the results are consistent with that reported.
Authors and Affiliations
Archana Verma, Mr. R. K. Bharti, Prof. R. K. Singh
Keywords
Related Articles
- EP ID EP649988
- DOI 10.24297/ijct.v4i1c.3121
- Views 96
- Downloads 0
Identification Of Hepatocellular Carcinoma Using Supervised Learning Algorithms
Analysis of diseases integrating multi-factors increases the complexity of the problem and therefore, development of frameworks for the analysis of diseases is an issue that is currently a topic of intense research. Due...
Communication Architecture design for an Interoperable Machine-to-Machine System
In recent years, we have witnessed a continuous increase in the number of embedded devices with communication capabilities that are changing the way we live, work and play. Smart grids, remote monitoring and control of...
Improvement inEnergy Efficiency of Wireless Sensor Network
Clustering in wireless sensor network is important to increase the lifetime of sensor network. LEACH protocol is one of the clustering routing protocols in wireless sensor networks. In LEACH each node has the equal proba...
Optimization of Constituents of (Ni, MO, Cu)/Kieselguhr Catalyst by Response Surface Methodology for Glycerol Production by Hydrogenolysis of Sucrose
Sucrose hydrogenolysis is industrially important forthe production of polyols. To provide high glycerol yieldunder milder reaction conditions, a nickel catalyst promotedby Molybdenum and copper supported on kieselguhr wa...
EVALUATION OF BITMAP INDEX USING PROTOTYPE DATA WAREHOUSE
Bitmap indices have become popular access methods for data warehouse applications and decision support systems with large amounts of read-mostly data. This paper could arrive a number of results such as ; Bitmap Index hi...