scholarly journals DNA sequence comparison based on Tabular Representation

2013 ◽  
Vol 4 (1) ◽  
pp. 172-175
Author(s):  
Archana Verma ◽  
Mr. R.K.Bharti ◽  
Prof. R.K. Singh
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Comparison ◽  
Sequence Similarity ◽  
Information Matrix ◽  
Similarity Score ◽  
Sequence Composition ◽  
Local Sequence ◽  
Dna Sequence Comparison ◽  
Similarity Scores

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.

A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases

2010 ◽  
Vol 2 (4) ◽  
pp. 1-11
Author(s):  
Dan Wei ◽  
Qingshan Jiang ◽  
Sheng Li
Keyword(s):  
Nucleic Acid ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Similarity ◽  
Similarity Analysis ◽  
Biological Sequence ◽  
Nucleic Acid Bases ◽  
New Approach ◽  
Characteristic Distribution ◽  
Sequence Similarity Analysis

Similarity analysis of DNA sequences is a fundamental research area in Bioinformatics. The characteristic distribution of L-tuple, which is the tuple of length L, reflects the valuable information contained in a biological sequence and thus may be used in DNA sequence similarity analysis. However, similarity analysis based on characteristic distribution of L-tuple is not effective for the comparison of highly conservative sequences. In this paper, a new similarity measurement approach based on Triplets of Nucleic Acid Bases (TNAB) is introduced for DNA sequence similarity analysis. The new approach characterizes both the content feature and position feature of a DNA sequence using the frequency and position of occurrence of TNAB in the sequence. The experimental results show that the approach based on TNAB is effective for analysing DNA sequence similarity.

scholarly journals Desulfovibrio africanus subsp. uniflagellum subsp. nov., a sulfate-reducing bacterium from a uranium-contaminated subsurface aquifer

2010 ◽  
Vol 60 (4) ◽  
pp. 880-886 ◽  
Author(s):  
I. Nydia Castañeda-Carrión ◽  
Cody S. Sheik ◽  
Lee R. Krumholz
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Type Strain ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Contaminated Site ◽  
Amino Acid Sequence Similarity ◽  
Trna Genes ◽  
Rrna Gene ◽  
Small Plasmid

The bacterial strain SR-1T was isolated from subsurface sediments of a uranium-contaminated site in Shiprock, New Mexico, USA. Cells are vibrioid and motile by means of a single polar flagellum. Strain SR-1T grows on sulfate, oxidizing formate, lactate and H2, but not malate, and ferments pyruvate. The DNA sequences of the 16S rRNA gene and the 16S–23S internal transcribed spacer of strain SR-1T showed 99.9 and 99.4 % similarity, respectively, to those of the type strain Desulfovibrio africanus DSM 2603T. The DNA sequence of the ITS region is 300 bases in length and contains two tRNA genes (tRNAIle, tRNAAla). The partial DNA sequence of the dsrAB gene showed 94.6 % amino acid sequence similarity to that of D. africanus. The DNA G+C content of strain SR-1T was 62.4 mol% and it showed 72 % DNA–DNA similarity to D. africanus. DNA typing methods that target gene clusters and whole genomes revealed characteristic genomic fingerprints for strain SR-1T. A small plasmid was detected by gel electrophoresis. On the basis of distinct phenotypic and genotypic characteristics, strain SR-1T represents a novel subspecies of D. africanus, for which the name Desulfovibrio africanus subsp. uniflagellum subsp. nov. is proposed. The type strain is SR-1T (=JCM 15510T =LS KCTC 5649T).

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