Journal of
Bioinformatics and Sequence Analysis

  • Abbreviation: J. Bioinform. Seq. Anal.
  • Language: English
  • ISSN: 2141-2464
  • DOI: 10.5897/JBSA
  • Start Year: 2009

JBSA Articles

July 2018

Evaluating the computing efficiencies (specificity and sensitivity) of graphics processing unit (GPU)-accelerated DNA sequence alignment tools against central processing unit (CPU) alignment tool

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...

Author(s): Shrikant Pawar, Aditya Stanam and Ying Zhu  

January 2018

Analysis of factors affecting codon usage bias in human papillomavirus

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...

Author(s): Takaaki Kamatani and Tatsuo Shirota

July 2016

In silico characterization of beta-galactosidase using computational tools

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...

Author(s): Gangadhar. C. Gouripur, Rohit. B. Kaliwal and Basappa. B. Kaliwal,

January 2015

Primer designing for PreS region of hepatitis B virus from the most conserved patches of hepatitis B virus genome

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...

Author(s): Naaz Abbas, Mohammad Ajmal and Talat Afroze

April 2014

Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA)

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...

Author(s): Eric S. Donkor, Nicholas T. K. D. Dayie, and Theophilus K Adiku

September 2013

Competitiveness of Ljubljana city

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...

Author(s): Art Kovačič

  • Article Number: 8D78AD72406

February 2013

Prediction of MHC Class II binders/non-binders using negative selection algorithm in vaccine designing

  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...

Author(s): S. S. Soam, Feroz Khan, Bharat Bhasker and B. N. Mishra

February 2013

In silico identification of miRNAs and their target prediction from Japanese encephalitis

  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...

Author(s): Vijay Laxmi Saxena and Alka Dwivedi

January 2013

MYCOsoft: A mycological database

  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...

Author(s): Ajit Kumar Saxena, Jyoti Gupta, S. Pandey, A. N. Gangopadhyay and L. K. Pandey

January 2013

Generation of a 3D model for human cereblon using comparative modelling

  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...

Author(s): Samina Bilal, Shumaila Barkat Ali, Sahar Fazal and Asif Mir

October 2012

Effect of physical activity on plasma metabonomics variation using 1H NMR, anthropometric and modeling methods

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...

Author(s): Mohammad Arjmand, Fatemeh Darvizeh, Ziba Akbari, Reyhaneh Mohabatiand Zahra Zamani

October 2012

Measurement of urinary calcium/creatinine and sodium/potassium excretion in healthy children aged 1-7 years in Imam Ali Hospital, Andimeshk in 2008

  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...

Author(s): Morad Rostami, Mohammad Aberomand, Alireza Khirollah and Masoomeh Jorfi

September 2011

Identification of unique repeated patterns, location of mutation in DNA finger printing using artificial intelligence technique

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...

Author(s):  B. Mukunthan, N. Nagaveni and A. Pushpalatha

  • Article Number: 58C31EF5603

September 2011

In silico analysis of amino acid sequences in relation to specificity and physiochemical properties of some aliphatic amidases and kynurenine formamidases

  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...

Author(s):   Naresh Kumar and T. C. Bhalla

  • Article Number: 548C10C5618

June 2011

Modern drug discovery process: An in silico approach

  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...

Author(s): V. Srinivasa Rao and K. Srinivas

  • Article Number: 6368F575575

June 2011

Protein ligand interaction analysis an insilico potential drug target identification in diabetes mellitus and nephropathy

Author(s): Satya vani Guttula, Allam Appa Rao, G. R. Sridhar and M. S. Chakravarthy

  • Article Number: 2F36E845584

May 2011

Information fusion and multiple classifiers for haplotype assembly problem from SNP fragments and related genotype

  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...

Author(s): M. Hossein Moeinzadeh and Ehsan Asgarian

May 2011

A framework for classification of antifreeze proteins in over wintering plants based on their sequence and structural features

  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...

Author(s): J. Muthukumaran, P. Manivel, M. Kannan, J. Jeyakanthan and R. Krishna

March 2011

Molecular docking studies on oxidosqualene cyclase with 4-piperidinopyridine and 4-piperidinopyrimidine as its inhibitors

  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...

Author(s): G. Jhansi Rani, M. Vinoth and P. Anitha  

  • Article Number: F8BC82B3076

March 2011

Polymorphisms in the transcription factor binding sites of host genes influences evolutionary susceptibility to falciparum malaria

  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...

Author(s): Tabish Qidwai, Prabhash K. Pandey, Sangram Singh and Farrukh Jamal

  • Article Number: F832BAB3106

February 2011

Avian influenza and micro RNA: Role of bioinformatics

  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...

Author(s): Pankaj Koparde and Shailza Singh

  • Article Number: DAFA6BF3025

February 2011

Evaluation of cassava mash dewatering methods

  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....

Author(s): Oladele Peter Kolawole, Leo Ayodeji Sunday Agbetoye and Agboola Simeon Ogunlowo

  • Article Number: 6D761403038

January 2011

Evolutionary analysis of gorilla, chimps and humans using sequence divergence

  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...

Author(s): Vibhu Ranjan Prasad, Soumya Chaurasia and Rao Sethumadhavan

  • Article Number: 97EEA132964

January 2011

Molecular docking of human histamine H1 receptor with chlorpheniramine to alleviate cat allergies

  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...

Author(s): Uma Maheshwari

  • Article Number: 1414ECD2980

December 2010

In silico sequence specific analysis of ERBB2 RTK alterations responsible for neuroectodermal tumors of Homo sapiens

  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...

Author(s):   Lakshmi P. T. V. and Subhashini S.  

  • Article Number: 799744C2910

December 2010

Nine linked SNPs found in goat melanophilin (mlph) gene

  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...

Author(s): Xiang-Long Li, Fu-Jun Feng, Rong-Yan Zhou, Lan-Hui Li, Hui-qin Zheng and Gui-ru Zheng

  • Article Number: E6842452924

October 2010

Insights into the key enzymes of secondary metabolites biosynthesis in Camellia sinensis

  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...

Author(s): Aditi Sharma, Ankita Punetha, Abhinav Grover and Durai Sundar

  • Article Number: 2AB0A762861

October 2010

UniDPlot: A software to detect weak similarities between two DNA sequences

  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...

Author(s): Marc Girondot, and Jean-Yves Sire

  • Article Number: BD4E9352879

August 2010

Evaluation of the risk of drug addiction with the help of fuzzy sets

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...

Author(s): Manoranjan Kumar Singh, L. Rakesh and Aniket Ranjan

August 2010

Toxicogenomics

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....

Author(s): S. Amala

July 2010

SEALI: A sequence alignment tool

  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...

Author(s): Manoj Giri, Dipti Jindal, Savita Kumari, Sarla Kumari, Devender Singh, Jawahar Lal and Neena Jaggi

  • Article Number: 464FDF82769

July 2010

In silico identification of potential horizontal gene transfer events between archaea and pathogenic bacteria

  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...

Author(s): Hasan Bilal Mirza, Maryam Anwar and S. Habib Bokhari

  • Article Number: 82336362789

June 2010

Structural characterization of pfSerine hydroxymethyltransferase: A novel target for malaria

  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...

Author(s): Rajasekhar Chikati, C. M. Anuradha, M. Chaitanya, B. Babajan, P. Yogi Prasad and Chitta Suresh Kumar.

  • Article Number: 52904702705

June 2010

QPSOBT: One codon usage optimization software for protein heterologous expression

  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...

Author(s): Yujie Cai, Jun Sun, Jie Wang , Yanrui Ding, Xiangru Liao and Wenbo Xu

  • Article Number: 1DB73052721

January 2010

Towards understanding the regulation of rubber biosynthesis: Insights into the initiator and elongator enzymes

  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...

Author(s): Ankita Punetha, Jayaraman Muthukumaran, Anmol Jaywant Hemrom, Nagarajan Arumugam, Mannu Jayakanthan and Durai Sundar

  • Article Number: 5231EED2579

January 2010

AIDGEN: A database Of AIDS information system

  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....

Author(s): Maruthamuthu Rajadurai, Sagadevan Arthy, M. Muthulakshmi and Shameela Rajam

  • Article Number: 0E0594F2584

December 2009

In silico effective inhibition of galtifloxacin on built Mtb-DNA gyrase

  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...

Author(s): D. Gowsia, B. Babajan, M. Chaitanya, C. Rajasekhar , P. Madhusudana,  C. M. Anuradha  , G. Ramakrishna,  K. R. S. Sambasiva Rao and Chitta Suresh Kumar

  • Article Number: ADC8B9A2554

December 2009

Sequencing and identification of homologous region encoding rust resistant-gene in soybean (Glycine max L.)

  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...

Author(s): Nguyen Thi Lang, Nguyen Cao Quan Binh and Bui Chi Buu

  • Article Number: 71C6A6D2560

October 2009

Choke point analysis of the metabolic pathways of Acinetobacter baylyi: A genomics approach to assess potential drug targets

  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...

Author(s): Shailza Singh, Priyanka Joshi and Balu Ananda Chopade

  • Article Number: 40109862508

October 2009

Bioinfotracker: A novel system for advanced genome functional insight

  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...

Author(s): Gopal Ramesh Kumar, Ganesan Aravindhan, Thankaswamy Kosalai Subazini and Radhakrishnan Sathish Kumar

  • Article Number: 1B8FFB52530

June 2009

Existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens

  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...

Author(s): Kandhavelu Meenakshisundaram, Lammi Carmen, Buccioni Michela, Dal Ben Diego, Volpini Rosaria, Marucci Gabriella

  • Article Number: 68FFD6E2450

May 2009

Synergies among different parts of sustainable development

  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...

Author(s): Art Kovačič

  • Article Number: 014F93A2253

May 2009

A computational technique for prediction and visualization of promoter regions in long human genomic sequences

  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...

Author(s): Q. M. Alfred, K. Bishayee, P. Roy and T. Ghosh

  • Article Number: 8A1E5372273

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