International Journal for Computational Biology (IJCB)
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Editorial Foreword
Get PDFThis issue of IJCB contains relevant paper of the Biomining’2014 Workshop held at the National Centre for Scientific and Technical Research (CNRST) Rabat-Morocco in September 2014. This Workshop on Biological and Genomics Data Mining 'Biomining2014' is organized by H3A Bioinformatics Network –Morocco with the participation of the Moroccan Classification Society and the Biotechnologies Laboratory of Mohammed V university-Rabat. The purpose of this event is to bring together researchers and practitioners interested in the application of computational systems and information technologies to the field of systems biology. This edition focuses on new developments in genome bioinformatics and computational biology for understanding biological processes
Analysis of Mass Spectrometry data: Significance Analysis of Microarrays for SELDI-MS Data in Proteomics
Get PDFMass Spectrometry (MS) has arguably become thecore technology in proteomics. MALDI and SELDI-TOFtechniques enable the study biological fluids, e.g. human blood.Analysis of these samples can lead to discover new biomarkerswhich can ease the diagnostic and prognostic of several diseases,e.g. various cancers. In this work, we focus on MS data fromSELDI-TOF experiments. We begin with a preprocessing step inorder to remove noises due to the acquisition process of the data.Then, we apply the differential analysis to a SELDI-MS data,using the Significance Analysis of Microarray (SAM) methodimplemented in Matlab. Results using the SAM method arecompared with those obtained by the conventional t-test andAnalysis Of Variance (ANOVA) in order to evaluate its efficacyand its performance. As a result, we demonstrate that the SAMmethod can be adapted for effective significance analysis ofSELDI-MS data. It is deemed powerful and provides betterresults that totes. An easy-to-use application is developed withMatlab for mass spectrometry data analysis from raw spectra todifferential analysis, including the SAM method
Alteration of Splicing Pattern on Angiotensin Converting Enzyme Gene Due To The Insertion of Alu elements
Get PDFAngiotensin Converting Enzyme (ACE) is a zinc metallopeptidase that has a significant role in blood pressure regulation and the pathophysiology of hypertension. ACE has two protein domains, the N-domain and the C-domain, which each has a single active site that functions independently of each other. There is insertion/deletion by 288 bp Alu elements in the intron 16 of ACE gene. The Alu elements potentially alter splicing process. The effect of the insertion of Alu elements in the splicing pattern of the ACE gene has not been reported. Here, we report on the results of splicing pattern analysis of the ACE gene due to the insertion of Alu elements. Using an in-silico approach, we found the presence of Alu elements insertion in intron 16 of ACE caused alternative splicing and experienced exonization. Further analysis showed that the exonization lead to a premature termination codon (PTC), which is raised protein shortening and lost one of its two protein domains. The loss of one protein domain may affect the catalytic activity of ACE. These findings suggest that the Alu elements I/D polymorphism is related to the differences in the catalytic activity of ACE that may influence blood pressure regulation and hypertension
Insilico Proteome Screening to Identify Prospective Drug Targets in Bacillus anthracis
Get PDFVarious Insilico based genome screening methods helped us in identifying the key drug targets for a pathogen. The accuracy of the predictions are systematically based on the benchmarks at different stages of methodology and the kind of dataset which is considered for the study. In the current study, we made an effort to screen the entire proteome of Bacillus anthracis for identification of putative drug targets. B. anthracis is the causautive agent for anthrax disease. Instead of genome sequence, the metabolically classified proteome of B. anthracis from JCVI-CMR database was considered for the present study. The entire proteome is been categorized into 25 different metabolisms and in each sub-categorised metabolisms respective protein sequences were retrieved and subjected to screening against Database of Essential Genes (DEG) and Human-Basic Local Alignment Search Tool (H-BLAST) databases. In total 136 essential genes/proteins were obtained from the DEGp (protein) screening whereas 145 Non-Human Homologs (NHHs) were predicted. The identified 145 NHHs are further subjected to criteria based selection to identify the most suitable, functional, putative drug targets. The 8 common hits of both DEG and H-BLAST were considered to be better potential targets as they justify the criteria of being an essential gene/protein, non-human homolog, availability of the 3D structure in PDB and having a significant functional role in the cellular biochemical processes.
Computational Structural Analysis of C-Terminal Residues of Proteins Containing Transmembrane Regions
Get PDFFor the past few years, the numbers of transmembrane protein structures in Protein Data Bank have been increased substantially. It is of interest to analyze the terminal residues of transmembrane proteins by using computational approaches. Also, up to our knowledge, no analysis was reported in the literature on the study of terminal residues in transmembrane proteins. While the N-terminal position of alpha and beta transmembrane proteins are composed of signal peptides, in the present work, a careful, in-depth, computational analysis such as residue preference, stability upon mutation, solvent accessibility, hydrogen bonding and carboxy terminal pentapeptide pattern search respectively has been done on C-terminal residues. Alanine in alpha transmembrane proteins and phenylalanine in beta transmembrane proteins are highly preferred. Glutamic acid and glycine residues can be substituted at the terminal sites of alpha and beta transmembrane proteins without affecting the protein's overall stability. Hydrogen bonding of terminal residues is studied in detail. Pattern search of carboxy pentapeptides shows that identical pentapeptides with reference to the position can adopt a different secondary structure. The results discussed in this paper may help to understand the role of carboxy terminal residues in alpha and beta transmembrane proteins. From our analysis, we insist that the preferences and structural analysis of carboxy terminal residues in alpha and beta transmembrane proteins, can help to model and design novel transmembrane proteins
The Emerging Roles of Human Immunity-Related GTPase M (IRGM) Gene
Get PDFImmunity-related GTPase family M (IRGM) protein, discovered for the first time in 1990, belongs to IRG family of proteins and is divided into five subfamilies (IRGA, IRGB, IRGC, IRGD and IRGM). These are responsive to interferon-g and play a pivotal role in immune response to pathogens in mice. Owing to lack of interferon response element in the promoter region, human IRGM does not respond to interferon-g stimulation, which is why it was earlier thought to be non-functional gene. Moreover, evolutionary history suggests that this gene was non-functional for ~25 million years ago. Bioinformatics has been instrumental in elucidating its evolutionary history as well as functions, especially in its interactions with the proteins of autophagy pathway. Recently, several studies have demonstrated the various functions of IRGM in limiting different pathogens in humans. This review discusses how and various roles played by IRGM unraveled in the recent years
Editorial Foreword
Get PDFWith the advancements in sequencing technologies and continuous developments in the area of computational and functional genomics and proteomics, there is a need to process this enormous amount of data to generate biologically meaningful information. The ultimate goal of bioinformatics is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. The central challenge is the rationalization of the mass of biological sequence information. The imperative that derives this analytical process is the need to convert sequence information into biochemical and biophysical knowledge, to decipher structural, functional and evolutionary clues latent in the language of biological sequences
Weighted Alignment Free Dissimilarity Metric for Promoter Sequence Comparison
Get PDFComparative sequence analysis has been a powerful tool in bioinformatics which interprets knowledge about the functionality of a sequence, making use of its structural information. Among the non coding regions of DNA, the comparison of promoter sequences has received a great deal of attention in medical science as promoter regions play a crucial role in gene regulation. In this work we propose an alignment free sequence comparison metric for comparison of promoter sequences. We use the binary and decimal position specific motif matrices (PSMM) of the promoters which were created for our experiments using the TFSEARCH tool. Simple weighted algorithm is used to compute the dissimilarity between the PSMMs of promoter sequences, thereby analyzing its underlying homology and functionality. The NCBI database was used to obtain the promoter sequences of 500 nucleotides upstream the transcription start site (TSS) of enzyme pyruvate kinase (PKLR) from the glycolysis pathway of different organisms for one experiment and all the enzymes from the glycolysis pathway of organism human for the other. The proposed dissimilarity metric is successful in bringing out differences on both the datasets and the results regarding similarities and differences in promoter sequences could be essential to have a clear knowledge of transcription regulation process in different organisms.The results reveal some useful findings which can be extended for a broader investigation
Three-Dimensional Cellular Automaton for Modeling the Hepatitis B Virus Infection
Get PDFHepatitis B is considered as the most common hepatic in the world and may lead to cirrhosis and liver cancer. It is caused by the hepatitis B virus, which attacks and can damage the liver. In this paper we investigate a new mathematical model to study the dynamic process of HBV infection on the liver. This model is based on a three dimensional cellular automaton, which is composed of four state variables. The model takes into account the heterogeneous feature and the spatial localization of the population studied. Furthemore, since the virus doesn’t remain only on the liver surface but penetrates into the organ, our model describes better the behavior of interactions between cells and hepatitis B virus in the liver than the previous works found in the literature, which have used only two cellular automata in their models
DPAAR: a Database of Perfect Amino Acid Repeat
Get PDFRepeat of amino acids in a protein sequence has clinical and functional importance. Perfect Amino Acid Repeat (PAAR) is a kind of relational as well as flat file database which is created by the comprehensive analysis of 5,42,782 protein sequences of Swiss-Prot database (released on 19th March,2014) to know the association between repeated sequence and disease. It provides the search engine for rapid access of a particular repeated amino acid, or particular swissprot ID, or particular length of repeated amino acids in a protein sequence. It also provides the flat files for single, oligo, and tandem repeated sequence information to get the complete informaton about concerned amino acids repeat. It consists of the tables of repeated sequence and its associated disease in human being