DeutJ: An ImageJ plugin for improved automatic masking and segmentation of images from confocal microscopy
February 2023
Due to advances in microscopic imaging, there are a plethora of biological molecules that can now be tagged and subsequentially imaged from almost any cell, organism, or tissue. However, the ability of software to analyze these images remains to be a challenge. ImageJ is open source software that allows for the processing of these images, but faces challenges when dealing with images that show weak contrast between...
Molecular organisation of Kell (KEL) red blood cell variants among voluntary blood donors at the National Blood Grouping Testing Laboratory, Kenya
October 2022
A variant is an alternative nucleotide located at a specific region of a gene. 48 genes encode for human red cell blood group systems. Variants within these genes encode for alleles, which can be highly polymorphic. The blood group gene loci jointly display all types of inherited variants to include single nucleotide variants (SNVs), insertions/deletions (indels), and structural variants. In Africa, there is limited...
Molecular characterisation of Duffy (FY) red blood cell variants among voluntary blood donors at the National Blood Grouping Testing Laboratory, Kenya
October 2022
A variant is an alternative nucleotide located at a specific region of a gene. 48 genes encode for human red cell blood group systems. Variants within these genes encode for alleles, which can be highly polymorphic. The blood group gene loci jointly display all types of inherited variants to include single nucleotide variants insertions/deletions and structural variants. In Africa, there is limited information on the...
Genomic profiles of Pseudomonas aeruginosa gene clusters based on profile HMMs, reveal novel therapeutic targets for clinical intervention
March 2021
Pseudomonas aeruginosa has developed antibiotic resistance, a major health concern worldwide, through different mechanisms including the formation of biofilms. Thus far, typing has been primarily assay based. However, the many sequences available from the US National Center for Biotechnology Information (NCBI) and the International Consortium of Pseudomonas Database (IPCD) offer alternative ways of characterizing the...
Computational characterization of providence virus non-structural proteins: Evolutionary and functional implications
March 2019
Providence virus is the only member of the family Carmotetraviridae and carries a positive single stranded RNA genome that encodes three open reading frames. The smallest open reading frame encodes the structural proteins. The largest open reading frame encodes a large putative protein, p130. The second overlapping open reading frame encodes two non-structural proteins; p40, a proposed accessory protein and p104, the...
Vitis vinifera gene expression differential analysis assessing microarrays data pre-processing dynamism by RNA-Seq approach
January 2019
Oligonucleotide microarrays data pre-processing procedures impacting gene expression differential survey performances were fully evoked. RNA-Seq tool exhibited high performances (sensitivity) as opposed to microarrays in transcriptomic as well as genomic studies. The aim of this study is to evaluate microarrays data pre-processing dynamism on gene expression differential analysis outcomes, assuming RNA-Seq approach as...
Evaluating the computing efficiencies (specificity and sensitivity) of graphics processing unit (GPU)-accelerated DNA sequence alignment tools against central processing unit (CPU) alignment tool
July 2018
Bioinformatics is an emerging field, where information technology usage can significantly accelerate life science research. It is a relatively new field and the scope of exploring new tools and techniques seems immense. One major field where bioinformatics plays important role is next generation sequence analysis (NGS), in which an unknown genome is shuttered into pieces and tried to align it to a reference known genome...
Analysis of factors affecting codon usage bias in human papillomavirus
January 2018
Indices of codon usage pattern of human papillomavirus (HPV) were analyzed to understand the key determinants of synonymous codon usage in the HPV genome. The complete sequences of 39 HPV genomes were downloaded from the website of the National Center for Biotechnology Information. The relative synonymous codon usage values, effective number of codons, GC content, percentage of GCs at the third position of synonymous...
In silico characterization of beta-galactosidase using computational tools
July 2016
β-galactosidase (EC.3.2.1.23) is an important enzyme, mainly used in the preparation of lactose hydrolyzed milk suitable for people with lactose intolerance. It is essential to understand the structural and functional aspects of various β-galactosidase produced from different sources. The present work deals with the use of bioinformatics to describe the physiochemical, functional and structural properties of...
Primer designing for PreS region of hepatitis B virus from the most conserved patches of hepatitis B virus genome
January 2015
The most conserved regions for 15 hepatitis B virus complete genome of different subtypes were aligned using PCGENE software CLUSTAL to design a new pair of primer that can bind to each subtype of hepatitis B virus (HBV), to amplify PreS region of HBV genome. A pair of primer from these conserved patches was selected using software PRIMER and named as Nhepf1 and Nhepr1. Nhepf1, forward primer bound 2362-2385 nucleotides...
Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA)
April 2014
Following advances in DNA and protein sequencing, the application of computational approaches in analysing biological data has become a very important aspect of biology. Evaluating similarities between biological sequences is crucial to our understanding of evolutionary biology, and this can be achieved by basic local alignment search tool (BLAST) and fast alignment (FASTA). BLAST and FASTA have become fundamental tools...
Competitiveness of Ljubljana city
September 2013
Ljubljana can be observed through different perspectives. Urban development is often written on the basis of economic level, social development, benchmarking results with similar economies, on the basis of past experiences. By urbanistic way of life we cover the main Slovenian areas in polycentric net, that is well organised in EU space. City is forced to lead a vital, beautiful and clean environment that supports...
In silico identification of miRNAs and their target prediction from Japanese encephalitis
February 2013
MicroRNA is a family of small non-coding RNAs that regulate gene expression in a sequence-specific manner. miRNAs are a class of post-transcriptional regulators. miRNAs are a family of 19 to 25 small nucleotide RNAs. Since miRNAs have been discovered and their role in gene regulation established, it has been theorized that viruses could generate miRNAs as well and that these viral encoded miRNAs could...
Prediction of MHC Class II binders/non-binders using negative selection algorithm in vaccine designing
February 2013
The identification of major histocompatibility complex (MHC) class-II restricted peptides is an important goal in human immunological research leading to peptide based vaccine designing. These MHC class II peptides are predominantly recognized by CD4+ T-helper cells, which when turned on, have profound immune regulatory effects. Thus, prediction of such MHC class-II binding peptide is very helpful towards...
Generation of a 3D model for human cereblon using comparative modelling
January 2013
Three-dimensional (3D) protein structures provide helpful insights into the molecularassociation of a gene, its purpose also allow efficient drug designing experiments, such as the structure-based design of specific inhibitors. Recently, it has been shown that protein (cereblon) is involved in various tissues and brain and is revealed to be related with mental retardation. After this first report of cereblon...
MYCOsoft: A mycological database
January 2013
The realization regarding the significance of microorganisms is increasing with the passage of time. In today’s scenario of global climate change and increasing threats to biodiversity, the wheel of advanced biotechnologies is revolving around microbes to restore the ecological balance lost in the past few decades. In Pakistan, however, we lack sufficiently reliable biological data to start with and our...
Measurement of urinary calcium/creatinine and sodium/potassium excretion in healthy children aged 1-7 years in Imam Ali Hospital, Andimeshk in 2008
October 2012
Due to the difficulty in obtaining a 24 h urine collection in children, a random sample of urine is often used to calculate the urine calcium to creatinine ratio. Also, urinary calcium excretion might be influenced by genetic, geographic area, etc. we decided to evaluate the urinary calcium, creatinine, sodium and potassium excretion in healthy children with 1-7 years and determine age-related reference...
Effect of physical activity on plasma metabonomics variation using 1H NMR, anthropometric and modeling methods
October 2012
The metabolic changes in serum during a sport program were explored using a metabonomic approach, based on proton nuclear magnetic resonance (1H-NMR) spectroscopy and anthropometry. The aim of this study was to classify two groups of female university students with body mass index over 25 kg/m², using multiple measured descriptors. The first group (n=16) underwent a complex and well programmed 18-week physical...
In silico analysis of amino acid sequences in relation to specificity and physiochemical properties of some aliphatic amidases and kynurenine formamidases
September 2011
Computational analysis of amino acid sequences of aliphatic amidases and kynurenine formamidases for some of their physiochemical properties and their substrate specificity has been done. Multiple sequence alignment of 18 amino acid sequences shows a clear difference between the two classes of aminohydrolases. Statistical analysis indicated a clear distinction between aliphatic amidases...
Identification of unique repeated patterns, location of mutation in DNA finger printing using artificial intelligence technique
September 2011
The proposed Neural-Fuzzy pattern recognition (NFPR) system discussed in this paper effectively reduces the complication in precisely analyzing and interpreting human deoxyribonucleic acid (DNA) sample. In this novel approach, the perfect blend made of bioinformatics and a competitive method of neural networks technique, which has the advantage over conventional computation technique, in...
Protein ligand interaction analysis an insilico potential drug target identification in diabetes mellitus and nephropathy
June 2011
Modern drug discovery process: An in silico approach
June 2011
Drug discovery process is a critical issue in the pharmaceutical industry since it is a very cost-effective and time consuming process to produce new drug potentials and enlarge the scope of diseases incurred. Drug target identification, being the first phase in drug discovery is becoming an overly time consuming process. In many cases, such produces inefficient results due to failure of conventional...
A framework for classification of antifreeze proteins in over wintering plants based on their sequence and structural features
May 2011
Overwintering plants produce antifreeze proteins (AFPs) which permits the plant survival in cold condition. Analysis of sequence and structural features of these proteins would help in better understanding of their functions. In this study, we report the analysis of 40 plant AFPs on the basis of sequence and structural based classification scheme (CS). Sequence based CS segregates the AFPs into various...
Information fusion and multiple classifiers for haplotype assembly problem from SNP fragments and related genotype
May 2011
Most positions of the human genome are typically invariant (99%) and only some positions (1%) are commonly invariant which are associated with complex genetic diseases. Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, due to the mutated form in human genome. Haplotype assembly is to divide aligned single nucleotide polymorphism (SNP) fragments, which is...
Molecular docking studies on oxidosqualene cyclase with 4-piperidinopyridine and 4-piperidinopyrimidine as its inhibitors
March 2011
Oxidosqualene cyclase (OSC) or Lanostrol Synthase is one of the major enzyme in cholesterol biosynthesis. OSC is involved in conversion of squalene to lanosterol. Increased level of cholesterol in blood leads to hypercholesterolemia and major risk factor for cardiovascular diseases. Statin drug molecule is developed to inhibit HMGCoA, which is the first enzyme of cholesterol biosynthesis showed major side...
Polymorphisms in the transcription factor binding sites of host genes influences evolutionary susceptibility to falciparum malaria
March 2011
Gene expression at the level of transcription is regulated by a set of transcription factors (TFs) that recognizes cis elements. We accessed the human promoters from eukaryotic promoter database. These sequences have been run in P-match tool. MEME software has been used for detection of conserved sequences in the promoter region. All the predicted known TFs and their binding sites along with weight...
Evaluation of cassava mash dewatering methods
February 2011
Using different cassava maturity age of 9, 12 and 15 months, evaluation study was carried out on cassava mash dewatering methods. Dewatering tanks with square and cylindrical shapes were made with steel for the experiment. Pressure devices from screw bolts, hydraulic jack press and rope / stick methods were used to squeezed cassava juice from the mash in the tanks. TMS 4(2) 1425 variety of cassava was used....
Avian influenza and micro RNA: Role of bioinformatics
February 2011
Avian influenza virus is a major cause of influenza all over the world. Influenza virus being a RNA virus shows high mutation rates, antigenic shift and drift. These phenomena contribute to ineffective chemotherapy against influenza viruses. Recent advances in the current therapy, drugs and vaccines are restricted with many factors such as toxicity, complexity, cost and resistance. New technologies...
Molecular docking of human histamine H1 receptor with chlorpheniramine to alleviate cat allergies
January 2011
Cat allergen Fel d 1, secreted by the cat’s sebaceous glands and that covers the cat’s skin and fur is the major cat allergen responsible for cat allergies in human. It interacts with and cross-links surface IgE antibodies on mast cells and basophils. Once the mast cell-antibody-antigen complex is formed, a complex series of events occurs that eventually leads to cell-degranulation and the release...
Evolutionary analysis of gorilla, chimps and humans using sequence divergence
January 2011
We have analyzed the sequence divergence amongst the three species that is, gorilla, chimpanzee and human varying from Hominidae and Pongidae. Apart from the genomic phylogeny, we compared the protein and rRNA phylogenies to increase the importance of phylogenetic analysis. The proteins selected are from the mitochondrial origin as mtDNA which codes for mitochondrial proteins, mutate at a higher rate compared...
Nine linked SNPs found in goat melanophilin (mlph) gene
December 2010
Melanophilin (mlph) gene was characterized as the candidate gene for dilute coat color in human, mice and dog, but little is known in goat. Nine linked SNPs were found in goat mlph gene by sequencing a total of 108 individuals from 5 goat populations. No homozygous mutation of the linked SNPs was detected, so we made a hypothesis that the mutation allele might be or might be linked with a recessive...
In silico sequence specific analysis of ERBB2 RTK alterations responsible for neuroectodermal tumors of Homo sapiens
December 2010
Current theories of oncogenesis suggest that tumors develop as a result of sequential alterations, which activate or inactivate tumor suppressor genes involved in the regulation of the cell cycle, and ultimately over express or suppress the proteins derived from those genes. Mutation is an obvious way of constitutive activation of a kinase. Owing to the importance of ERBB proteins in both...
UniDPlot: A software to detect weak similarities between two DNA sequences
October 2010
Search for DNA sequence similarity is a crucial step in many evolutionary analyses and several bioinformatic tools are available to fulfill this task. Basic local alignment search tool (BLAST) is the most commonly and highly efficient algorithm used. However, it often fails in identifying sequences showing very weak similarity. An alternative method is to use Dot Plot, but such a graphical method is not...
Insights into the key enzymes of secondary metabolites biosynthesis in Camellia sinensis
October 2010
Tea is one of the most popular beverages consumed throughout the world. It is a source of important secondary metabolites like monoterpenoids, carotenoids and catechins. Monoterpenoids and carotenoids are important constituents of tea aroma. The formation of tea aroma involves synthesis and release of volatile monoterpenoids and carotenoids. On the other hand, catechins are responsible for the beneficial...
Toxicogenomics
August 2010
The field of toxicology is defined as the study of stressors and their adverse effects. One discipline should deals with hazard identification, mechanistic toxicology, and risk assessment. Thus emerge a new field called toxicogenomics. Toxicogenomics is a rapidly developing discipline that promises to aid scientists in understanding the molecular and cellular effects of chemicals in biological systems....
Evaluation of the risk of drug addiction with the help of fuzzy sets
August 2010
The primary focus of this paper is to present a general view of the current applications of fuzzy logic in medical analogy of consumption of drugs. The paper also deals with the origin, structure and composition of fuzzy sets. The authors particularly review the medical literature using fuzzy logic. Fuzzy set theory can be considered as a suitable formalism to deal with the imprecision intrinsic to many...
In silico identification of potential horizontal gene transfer events between archaea and pathogenic bacteria
July 2010
Horizontal gene transfer plays a potent role in the evolution of prokaryotes. A rigorous sequence and phylogenetic analysis was carried out using the robust clustalW, motifs/domains finding suites and neighbor-joining based ProtDist and BioNJ. This paper reports a few cases of horizontal gene transfer events between archaea and bacteria. Some of these events have been found to be unique to the bacterial...
SEALI: A sequence alignment tool
July 2010
In this paper we propose a novel program for sequence alignment. This program has been developed in PERL. The web interface uses CGI and front end for data input and viewing the result has also been developed. This program counts the length of two sequences, aligns the two sequences, counts the number of matches, mismatches, gaps and score and displays the possible alignment. Key...
QPSOBT: One codon usage optimization software for protein heterologous expression
June 2010
QPSOBT is a codon usage optimization software based on the Quantum-behaved Particle Swarm Optimization (QPSO) algorithm. It can design synthetic genes of multikilobase sequences for protein heterologous expression rapidly. The program runs on .NET platform. Compared to the existing codon optimization software and web services, QPSOBT is able to generate better results when DNA/RNA sequence length is less than...
Structural characterization of pfSerine hydroxymethyltransferase: A novel target for malaria
June 2010
New chemotherapeutic targets are urgently required to control malaria, a tropical disease caused by Plasmodium sp., which has been haunting mankind for ages. Serine hydroxymethyltransferase (SHMT) plays a major role in DNA biosynthesis.PfSHMT sequence compared for identities with hu mtSHMT (2A7V), T.ThHb8SHMT (2DKJ) and Rabbit cytSHMT (1EQB). ClustralW and Modeller9v3 were used for multiple...
AIDGEN: A database Of AIDS information system
January 2010
AIDS is a a highly vulnerable life threatening disease that attacks and destroys the body’s immune system, leaving the patient abnormally vulnerable to infections and many other diseases caused by the human immunodeficiency virus (HIV) in humans. The overall aim of this AIDGEN database is to create awareness among people about AIDS, to dispel myths about AIDS and AIDS causing genes....
Towards understanding the regulation of rubber biosynthesis: Insights into the initiator and elongator enzymes
January 2010
Natural rubber is an important polymer produced by plants and made up of isoprene units derived from isopentenyl diphosphate (IPP). Although more than 2000 plant species are known to produce natural rubber, currently there are two important commercial sources, Hevea brasiliensis (the Brazilian rubber tree) andParthenium argentatum Gray (guayule). Natural rubber biosynthesis requires three distinct...
Sequencing and identification of homologous region encoding rust resistant-gene in soybean (Glycine max L.)
December 2009
Soybean (Glycine max L.) is one of the most important crops that is both easily cultivated and of high efficiency. Its product is commonly used as fresh-seed directly or produced into plant oil, cake, candy and milk. It can also be processed as feed for domestic animals for enhancing the protein requirement in daily meals, and it can be exported for providing valuable currency resource. On the other...
In silico effective inhibition of galtifloxacin on built Mtb-DNA gyrase
December 2009
Tuberculosis (TB) resurged in the late 1980s and now kills approximately 3 million people a year. The reemergence of tuberculosis as a public health threat has created a need to develop new anti-mycobacterial agents. The Mtb-DNA Gyrase is an attractive target for development of new drugs due to its indispensable role in catalyzing the negative supercoiling of DNA and is essential for efficient DNA...
Bioinfotracker: A novel system for advanced genome functional insight
October 2009
With the accelerated accumulation of genomic sequence data in the World Wide Web, it has become highly essential to understand the role of these sequences in the biological systems by incorporating various advanced research archetypes. The intricacy of handling such a huge dataset manually has increased the need to develop automated methods that can analyze enormous numbers of biological sequences and produce...
Choke point analysis of the metabolic pathways of Acinetobacter baylyi: A genomics approach to assess potential drug targets
October 2009
Numerous species of the genus Acinetobacter have been known to cause various nosocomial infections. An insight into the pathogenesis of Acinetobacter baylyireveals that it is a potent organism in causing nosocomial infections. In this study, choke point analysis of the entire metabolic network of A. baylyi is performed to assess potential drug targets. Potential drug targets are...
Existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens
June 2009
Comparative genomic analysis constitutes a powerful approach for the systematic understanding of genome. The comparative and evolutionary analysis of known microRNAs in Homo sapiens elucidates the discovery of the existence of the novel non-coding RNA, which is transcribed from the unique gene precursor and produces three different non coding RNAs such as piRNA, snoRNA and microRNA. This new...
Synergies among different parts of sustainable development
May 2009
Sustainable development became an important paradigm in new EU countries. In new member countries can be seen the development of tools for measuring sustainable development. Sustainable development can be measured on many ways. In the paper we will show the evaluation of main determinants of sustainable development. Normally more developed countries have a higher sustainability readiness. In the paper the...
A computational technique for prediction and visualization of promoter regions in long human genomic sequences
May 2009
This communication proposes a simple algorithm with high specificity and sensitivity for determining promoter regions in human genomic sequences. This method relies upon non-redundant and experimentally verified promoter data sets form Eukaryotic Promoter Database (EPD) as training parameters. This technique predicts and computationally satisfies the promoter regions in the NCBI annotated database...
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