Journal of Computer Science & Systems Biology

This paper proposes two different approaches to tracks two occlusion targets. Occlusion means hiding an object by another object. In this paper, two approaches are devised to handle the occlusion detection. In a video, during the tracking process, the states of the object are gradually adjusted one by one to eliminate the occlusion effects. The edges are detected and identified whether the occlusion is partial or full. Spatial approach is used to handle partial occlusion and temporal approach is used to handle full occlusion detection. The spatial approach uses edge-based restoration scheme that 1) identifies areas that are likely to contain wrong motion vectors, 2) finds artifacts within these areas, and 3) restores these artifacts. The temporal approach is planned to fill the missing parts from the past history of a person if available.

Previous studies of properties of metabolic works have mainly focused on the statistic properties of networks, including the small world, and power-law distribution of node degree, and building block of network motifs. Symmetry in the metabolic networks has not been systematically investigated. In this report, symmetry in directed graph was introduced and an algorithm to calculate symmetry in directed and disconnected graphs was developed. We calculated several indices to measure the degree of symmetry and compared them with random networks. We showed that metabolic networks in KEGG and BioCyc databases are generally symmetric and in particular locally symmetric. We found that symmetry in metabolic networks is distinctly higher than that in random networks. We obtained all the orbits in networks which are defined as structurally equivalent nodes and found that compound pairs in the same orbit show much more similarity in chemical structures and function than random compound pairs in network, which suggests that symmetry in the metabolic network can generate the functional redundancy, increase the robustness and play an important role in network structure, function and evolution.

The polymerase chain reaction (PCR) is an enzymatic reaction which follows simple, predictable and well understood principles. Selective amplification of nucleic acid molecules, that are initially present in minute quantities, provides a powerful tool for analyzing nucleic acids. In this context, efficiency and sensitivity of the PCR largely depends on the efficiency of the primers that are employed for the amplification of a concerned gene. Environmental adversities like drought resulting in scarcity of water have detrimental effects on crop yields worldwide. Sustainable agricultural and food productivity requires development of stress resistant plant species like drought resistant crops that can with stand and flourish in scanty water level environments. A key to underlying such attempts is the molecular understanding of the discrete stress processes that are interwoven at multiple levels. In this review, we discuss about some of the contemporary developments in the area of stress resistance by plants along with the various approaches for the PCR primer designing of two key genes involved in drought resistance, DREB1A and DREB2A.

Previously we have reported a microarray image processing and data analysis package Matarray, where quality scores are defined for every spot that reflect the reliability and variability of the data acquired from each spot. In this article we present a new development in Matarray, where the quality scores are incorporated as weights in the statistical evaluation and data mining of microarray data. With this approach filtering of poor quality data is automatically achieved through the reduction in their weights, thereby eliminating the need to manually flag or remove bad data points, as well as the problem of missing values. More significantly, utilizing a set of control clones spiked in at known input ratios ranging from 1:30 to 30:1, we find that the quality-weighted statistics leads to more accurate gene expression measurements and more sensitive detection of their changes with significantly lower type II error rates. Further, we have applied the quality-weighted clustering to a time- course microarray data set, and find that the new algorithm improves grouping accuracy. In summary, incorporating quantitative quality measure of microarray data as weight in complex data analysis leads to improved reliability and convenience. In addition it provides a practical way to deal with the missing value issue in establishing automatic statistical tests.

There is rising death of humans worldwide by reason of tuberculosis. The current sequencing of the Mycobacteriumtuberculosis genome holds assure for the development of new vaccines and the design of new drugs. In this view, the functions prediction of genomic sequences for hypothetical proteins will invigorate our knowledge with reference to the identification of new drugs for tuberculosis. There are various function prediction methods available based on the on the assumption. The process accurate annotation for genes in newly sequenced genomes currently has been based on sequence similarity. In this work about 250 hypothetical proteins of Mycobacteriumtuberculosis taken functions were predicted using Bioinformatics web tools, BLAST, INTERPROSCAN, PFAM and COGs.

Discerning how different major groups of organisms are related to each other and tracing their evolution from the common ancestor remains controversial and unsolved. In recent years, much new information based on a large number of gene and protein sequences has become available. So far phylogenetic analysis can be carried out based on either nucleic acid or protein sequences. However it was become evident that both approaches have a many serious limitations and pitfalls. Our novel findings follows from analysis of loops in elongation factors EF1A using novel informative characteristic which was called “loops” method. The method is based on the ability of amino acid sequences form loops in protein structure. The specificity of a criterion for grouping organisms is distinctly evident from the analysis of the loops using EF1A for three kingdoms of life. Each kingdom displayed variations in the number of loops and their location within the three EF1À domains and can be consider as imprint of molecular evolution. Stronger support that animals and fungi are sibling kingdoms was found.

Structure-based lead optimization approaches are increasingly playing a role in the drug-discovery process. Virtual screening by molecular docking has become a largely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available. The performance of two docking programs (Arguslab and Surflex), for virtual database screening, is studied. Surflex is well recognized commercial package while Arguslab is distributed freely for Windows platforms by Planaria Software. Comparisons of these docking programs and scoring functions using a large and diverse data set of pharmaceutically interesting targets and active compounds are carried out. We focus on the problem of docking and scoring flexible compounds which are sterically capable of docking into a rigid conformation of the receptor. The three dimensional structures of a carefully chosen set of 300 pharmaceutically relevant protein-ligand complexes were used for the comparative study. The results show that Surflex outperforms largely Arguslab in all tests studied.

The present paper aims to identify the distribution of Microsatellite markers (SSRs)/Single Nucleotide Polymorphism (SNPs) as resource tools for the analysis of interspecies hypervariability in Prosopis spp. Microsatellites are ubiquitously repeated extension of 1-5 bp motif extended throughout the genome. The dbEST division of Genbank contains 1467 ESTs of Prosopis juliflora which have been utilized for the development of genic microsatellite markers (SSRs). Locally installed assembling program was used for the cluster analysis of the EST. Analysis was performed on a Linux Cluster system. The analysis of the putative unigenes has been shown to have most abundant motif of A/T followed by dinucleotide AG/CT and trinucleotide repeat AAG/CTT. EST-derived SNPs are becoming the resources for the development of SNP markers. The relative rates of development of the high throughput computational methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has gained wide applications in the field of the molecular markers.

The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity. The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock. However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate. Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate. Here it is shown that the equidistance result remains valid even when different species can be independently shown to have different mutation rates. A random sampling of 50 proteins shows that nearly all proteins display the equidistance result despite the fact that many proteins have nonconstant mutation rates. Therefore, the genetic equidistance result does not necessarily mean a constant mutation rate. Observations of different mutation rates do not invalidate the genetic equidistance result. New ideas are needed to explain the genetic equidistance result that must grant different mutation rates to different species and must be independently testable.

Whole genome sequences of the four strains of Streptococcus pneumoniae, encapsulated TIGR4, D39, G54 and nonencapsulated R6 are considered for the comparative study on genome features, whole genome pairwise alignment, gene role category, and virulence factors using relevant comparative genomics tools. The study of capsular polysaccharide synthesizing genes reveals that many cps genes are unique to TIGR4, which shows the high virulence nature of TIGR4. Further, the study on the other virulence factors such as pneumococcal surface protein A, autolysin, hyaluronate lyase, pneumolysin, neuraminidase B, and pneumococcal surface antigen A of TIGR4 are much related to those of the other three strains, and hence the virulence nature due to these factors among four strains seems to be similar. But it differs from neuraminidase A, choline binding protein A and immunoglobulin A1 protease. Also in the present study, 4 and 22 hypothetical protein sequences of TIGR4 and R6 respectively are predicted as virulence factors. Among those sequences, it is found that 8 hypothetical protein sequences with 7 different functional regions of R6 are related to other previously known virulence factors of TIGR4 and R6 of S. pneumoniae.

The present study undertaken to predict the three dimensional structure and active site analysis of inducible serine protease inhibitor -2(ISPI -2) known to inhibit the activity of entomopathogenic fungi Metarhizium anisopliae in Galleria mellonella a severe pest of most economic important crops. This inhibitor completely inactivates serine protease produced by M.anisopliae which acts as major virulent factor for G.mellonella and imparts natural immunity to the pest. Initially, the structural template for G.mellonella – ISPI-2 was identified from structural database using homology modeling or comparative modeling approach. Based on the knowledge of the template, a three-dimensional model was predicted and processed in to energy minimization, Ramachandran plot analysis, quality assessment and finally deposited into Protein Model Database. An active site of the theoretical model was analyzed and helpful to recognize the effective ligands.

DNA vaccines have been used with great success in experimental and some clinical therapy. However, the mechanisms of activation of the immune system by these vaccines are not utterly understood yet. Hsp65 is aMycobacterium leprae chaperone whose gene has been efficiently used as experimental DNA vaccine against tuberculosis and clinical trial against tumor. Since little is know about the three-dimensional (3D) structure of hsp65 and modeling of 3D protein structure can increase the information to improve the knowledge about the mechanism action as well as the design of new DNA vaccine formulation, here we used the bioinformatics to get the design in silico of hsp65 (heat shock protein) molecule. The determination of hsp65 3D structure was obtained by homology using the software Modeller (Eswar et al., 2001). It was used two proteins as models: 1SJP, a 60- kDa chaperonin from Mycobacterium tuberculosis in the PDB, and the 1WE3, the crystal structure of the chaperonin complex Cpn60/Cpn10/(ADP)7 from Thermus thermophilus). Our results showed an interesting structure in Hsp65 that could be important in development or modulation of immune response.

High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multigigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem’s SOLiD (sequencing-by-ligation). enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stop codons, and splice isoforms. Variant detection is aided by the ability to filter variant calls dynamically based on consistency, expected allele frequency, sequence quality, coverage, and variant type in order to minimize false positives while maximizing the identification of true positives. also enables comparisons of genes with variants between cases and controls or bulk segregant pools. Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.