International Journal of Bioinformatics Research

200-201

Authors: RAJASEKARAN E., VIJAYASARATHY M

Alanine aminotransferase (ALT) is an enzymatic protein involved in catabolism of amino acids. The carbon distribution study on this clinically important protein is carried out here. The study reveals that the carbon content is generally higher than the expected values of 31.45%. The alteration in carbon content other than the active site might improve the activity of this enzymatic protein. Particularly the reduction at the carboxyl end of the sequence is more appropriate. Carbon distribution analysis clearly locates the active site of ALT protein, which is reported here.

207-213

Authors: SOUMEN KR. PATI, ASIT KR. DAS

DNA microarray technology is a fundamental tool in gene expression data analysis. The collection of datasets from the technology has underscored the need for quantitative analytical tools to examine such data. Due to the large number of genes and complex gene regulation networks, clustering is a useful exploratory technique for analyzing these data. Many clustering algorithms have been proposed to analyze microarray gene expression data, but very few of them evaluate the quality of the clusters. In this paper, a novel cluster analysis technique has been proposed without considering number of clusters a priori. The method computes a similarity measurement function based on which the clusters are merged and subsequently splits a cluster by computing the degree of separation of the cluster. The process of splitting and merging performs iteratively until the cluster validity index (i.e. DB index) degrades. The experimental result shows that the proposed cluster analysis technique gives comparable results on gene cancer dataset with existing methods. This study may help raise relevant issues in the extraction of meaningful biological information from microarray expression data.

221-226

Authors: SINGH V.K., SINGH A.K., CHAND R., KUSHWAHA C.

Bioinformatics is an interdisciplinary area of the science composed of biology, mathematics and computer science. Bioinformatics is the application of information technology to manage biological data that helps in decoding plant genomes. During the last two decades enormous data has been generated in biological science, firstly, with the onset of sequencing the genomes of model organisms and, secondly, rapid application of high throughput experimental techniques in laboratory research. Biological research that earlier used to start in laboratories, fields and plant clinics is now starts at the computational level using computers (In-silico) for analysis of the data, experiment planning and hypothesis development. Bioinformatics develops algorithms and suitable data analysis tools to infer the information and make discoveries. Application of various bioinformatics tools in biological research enables storage, retrieval, analysis, annotation and visualization of results and promotes better understanding of biological system in fullness. This will help in plant health care based disease diagnosis to improve the quality of Plant.

236-240

Authors: ROHIT SHARMA, RANJIT SINGH

The purpose of this study was to investigate the effects of three basic cyclic rhythms called biorhythms including a 23-day physical cycle, a 28-day emotional cycle and a 33-day intellectual cycle on the incidence of accidents in Agra casting manufacturing units. For this purpose a sample of 462 accidents were randomly selected for the analysis. The statistical methods chi-square of significance level p<0.05and 95%CI were used to determine the significance of the study. Results of the study showed that Chi-square values were significant at p<0.05 in all the cases except in the case of serious accidents as response of results were mixed but the value of 95%CI is significant in all the cases as the values were much more than expected to occur on critical days purely by chance 20.4%. It was found, using alternative definition 4 of the critical days that 67.2% of accidents in case of total number of accidents examined and 72.8% of accidents in case of serious accidents were occurring on critical days for the various combinations of alternative critical days definition, which were higher than the other alternative definitions of critical days. Present work suggested that biorhythm theory acts as an information system and may be implemented in the industries in which chances of workers to get stuck with accidents are more. Relevance to industry-Some industrial activities involve lifting and carrying heavy loads or working in dusty, fummy, and heated environment. Such tasks may lead to various types of accidents to the workers. This study investigated the effects of biorhythm on industrial accidents, so that the workers could be kept away from the hazardous tasks on critical days. The results may provide useful information for further study in the prevention of industrial accidents.

103-113

Authors: SUBHALAXMI NAYAK, UMADEVI K., REDDY M.N.

Lung cancer is a disease of uncontrolled cell growth in tissues of the lung. This growth may lead to metastasis, which is the invasion of adjacent tissue and infiltration beyond the lungs. The vast majority of primary lung cancers are carcinomas of the lung, derived from epithelial cells. Therefore, the present study is aimed at detecting the highly expressed genes, responsible for lung cancer through Serial Analysis of Genome Expression (SAGE) Genie at Cancer Genome Anatomy Project (CGAP). IGL@ (Immunoglobulin lambda locus) gene is predominantly highly expressed in the lung cancer and is considered to be a new target for the Cancerous diseases. The protein was retrieved from the Swissprot/Uniprot KB with accession number Q6GMX3 and was modelled using MODELLER9v7 for predicting the 3D structure of the IGL @ protein which provides an accurate and efficient module to build loops and side chains, found to be identical in sequence. Modelled structure revealed appreciable measures when subjected to structure verification and evaluation using PROCHECK. Ramachandran plot signified the present work undertaken through conformational parameters ? (phi) and ? (psi) angles calculated from model with 93.4% residues in most favoured region. Further, PROCHECK results confirmed acceptance of model through main and side-chain values. Root mean square distance of planarity was found below 0.02. Hence the model was revealed to have good stereochemistry. Structure of IGL@ Protein can be important tool for future endeavours towards structure based drug designing techniques to impel the search of new efficient inhibitors.

118-134

Authors: VALLI G., LALITHISWARI T., JOTHIMALAR S., RAJESWARI N.

N-Oxides were found to have antimicrobial activity. In continuation of our work on synthesis, characterization and biological activities (in vitro method) of N-Oxides and knowing their biological activities against micro organisms, we have correlated the biological activity of these N-Oxides against the micro organisms like Staphylococcus aureus, Salmonella typhi "H", Escherichia Coli, Pseudomonas aeruginosa, Klebsiella aerogenes, Enterobacteraerogenes, Citrobacter, Staphylococcus epidermidis, and Aeromonas hydrophila by Insilico method. The target molecules (microorganism) were taken from Protein data bank. Various soft wares were used to find out the drug likeness properties of these N-Oxides. Online software "Molinspiration" was used to calculate log P (ie) Hydrophobicity of a drug. ACD/ Chemsketch was used to draw the structures of N-Oxides. Hex 4.2, docking software was used to predict the drug activities of these N-Oxides. The drug activities were measured in terms of drug likeness property by recording the E-Total value and compared with the marketed standard drugs for the above micro organism infections. Standard drugs were taken from drug bank. As per the standard norms, it was observed that the compounds that have negative E-Total values could be used as a drug. We have selected Ceftazidime ,Cefepime and Ceftizoxime as standard drugs among the available drugs for these microorganism for correlating the drug activities of these N-Oxides. We observed that some of our N-Oxides were found to have higher drug activities compared to standard drugs.

142-147

Authors: SRIDHAR RAMACHANDRAN

Background: There is substantial evidence that replication-based nucleotide substitutions in primates occur more frequently in males than in females. There has been disagreement about the extent of this disparity. The human Alu repeats provide an ideal mechanism to further investigate the degree of replication-based error by providing tighter statistical boundaries on the male-to-female mutation ratio, α, in humans. Results: We analyze patterns of point mutations in Alu repeats across the entire human genome in order to elucidate the processes of mutation and fixation. This analysis provides substantial statistically bounded support for the accumulation of more point mutations in the Y chromosome compared to the X chromosome. We report a 99.99% confidence interval for human α between 1.280 and 1.289. Our results suggest that compared with eggs, sperm tend to carry a greater number of point mutations accumulated primarily during the production of gametes. Conclusion: Our results suggest that although mutation may be primarily replication driven (as previous studies suggest) the observed value of α does not exceed the threshold necessary to conclude that contributions of replication independent factors are negligible.

161-166

Authors: QIU CHEN, KOJI KOTANI, FEIFEI LEE, TADAHIRO OHMI

DNA sequence search is a fundamental topic in bioinformatics. The Smith-Waterman algorithm achieved highest accuracy among various sequence alignment tools, but it usually spends much computational time to search on large DNA sequence database. On the contrary, BLAST and FASTA have improved the search speed by using heuristic approaches, by there is a possibility of missing an alignment or giving inaccurate output. This paper presents an efficient hierarchical method to improve the search speed while the accurate is being kept constant. For a given query sequence, firstly, a fast histogram based method is used to scan the sequences in the database. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith-Waterman algorithm is then applied to each remainder sequences. Experimental results show the proposed method combining histogram information and Smith-Waterman algorithm is a more efficient algorithm for DNA sequence search.

178-184

Authors: ASHISH RUNTHALA, ANKITASH TULYANI, DHIRAJ SHARMA, MAHAVEER SINGH

Fermentation products are indigenous to many civilizations, and they have been produced by industries since a long time. Saccharomyces cerevisiae S288C (commonly known as baker's yeast) is the strain mainly used in the Glucose based fermentation industries. We have seen the use of same yeast strain at different places with different Phenotypic Constraints. The way to improve the adaptability of considered strain for desired phenotypic conditions, using smart selection of genes through cybernetic modeling is illustrated. Phylogenetic homologues for all S. cerevisiae S288c Glucose Fermentation pathway genes were screened to search evolutionarily related functional domains in other yeast strains like Saccharomyces cerevisiae YJM789, Candida glabrata CBS138, Kluyveromyces lactis NRRL Y-1140, Ashbya gossypii ATCC10895 etc., which are adapted naturally in different set of environment. We observed that Saccharomyces cerevisiae YJM789, Candida glabrata CBS138, Ashbya gossypii ATCC10895, Kluyveromyces lactis NRRL Y-1140 possess highly conserved functional domains, which can be carefully selected based on usage. This study aims at designing an algorithm to select and incorporate evolutionary homologues for genes of a considered strain, which mostly show sub-optimal performance in the desired set of experimental constraints. Such a consideration of native icroenvironment and volutionary closeness in the selection of functional homologues of the entire genetic set can thus be significantly fruitful.

190-193

Authors: ZHONGYANG TAN, GUANGMING ZENG, MING CHEN, MINGFU LI

More and more computational resources for microRNAs (miRNAs) have been developed in recent years. That may lead to selective difficulty, mistakes of usage and confusion due to their confined scope of usage. Here, we summarize and classify the knowledge that has been accumulated in the fields and present a novel tool, MRST (miRNA resource store tool), for the storage of miRNA resources.