Bioinformation (Bioinformation)

Publications in this journal

• Article: Graphical Contig Analyzer for All Sequencing Platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes

  Rommel Thiago Jucá Ramos, Adriana R. Carneiro, Pablo H. Caracciolo, Vasco Azevedo, Maria Paula C. Schneider, Debmalya Barh, Artur Silva
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  ABSTRACT: Accepted article:
  Bioinformation 08/2013; Accepted.
• Article: Search for signatures in miRNAs associated with cancer

  Ram Ko, Sumit Biswas
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  ABSTRACT: Since the first discovery in the early 1990’s, the predicted and validated population of microRNAs (miRNAs or miRs) has grown significantly. These small (~22 nucleotides long) regulators of gene expression have been implicated and associated with several genes in the cancer pathway as well. Globally, the identification and verification of microRNAs as biomarkers for cancer cell types has been the area of thrust for most miRNA biologists. However, there has been a noticeable vacuum when it comes to identifying a common signature or trademark that could be used to demarcate a miR to be associated with the development or suppression of cancer. To answer these queries, we report an in silico study involving the identification of global signatures in experimentally validated microRNAs which have been associated with cancer. This study has thrown light on the presence of significant common signatures, viz., - sequential and hybridization, which may distinguish a miR to be associated with cancer. Based on our analysis, we suggest the utility of such signatures in the design and development of algorithms for prediction of miRs involved in the cancer pathway.
  Bioinformation 06/2013; 9(10).
• Article: Resistome analysis of Mycobacterium tuberculosis: Identification of aminoglycoside 2’-N-acetyltransferase (AAC) as co-target for drug desigining

  Rakesh S Joshi, Mahendra D Jamdhade, Mahesh S Sonawane2 & Ashok P Giri
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  ABSTRACT: The emergence of multidrug resistant tuberculosis (MDRTB) highlights the urgent need to understand the mechanisms of resistance to the drugs and to develop a new arena of therapeutics to treat the disease. Ethambutol, isonazid, pyrazinamide, rifampicin are first line of drugs against TB, whereas aminoglycoside, polypeptides, fluoroquinolone, ethionamide are important second line of bactericidal drugs used to treat MDRTB, and resistance to one or both of these drugs are defining characteristic of extensively drug resistant TB. We retrieved 1,221 resistant genes from Antibiotic Resistance Gene Database (ARDB), which are responsible for resistance against first and second line antibiotics used in treatment of Mycobacterium tuberculosis infection. From network analysis of these resistance genes, 53 genes were found to be common. Phylogenetic analysis shows that more than 60% of these genes code for acetyltransferase. Acetyltransferases detoxify antibiotics by acetylation, this mechanism plays central role in antibiotic resistance. Seven acetyltransferase (AT-1 to AT-7) were selected from phylogenetic analysis. Structural alignment shows that these acetyltransferases share common ancestral core, which can be used as a template for structure based drug designing. From STRING analysis it is found that acetyltransferase interact with 10 different proteins and it shows that, all these interaction were specific to M. tuberculosis. These results have important implications in designing new therapeutic strategies with acetyltransferase as lead co-target to combat against MDR as well as Extreme drug resistant (XDR) tuberculosis.
  Bioinformation 02/2013;
• Article: Prevalence of hyperhomocysteinemia in healthy Indian doctors

  Sandesh Kamdi, Prashant Palkar
  Bioinformation 02/2013; 9(4).
• Article: The Whole Genome Expression Analysis in two Microarray Technologies toIdentify Gene Networks That Mediate the Myocardial Phenotype of CD36 Deficiency

  Sabaouni I, Ibrahimi A, Moussa A, Vannier B
  Bioinformation 01/2013;
• Article: Computational analysis of bovine alpha-1 collagen sequences.

  Ayan Saha, Md Jibran Alam, Kutub Uddin Muhammad Ashraf, Adnan Mannan
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  ABSTRACT: Bovine collagen alpha-1 is a naturally occurring extracellular matrix protein found in tendons and other connective tissues. It plays a vital role in cell growth, differentiation, attachment, and migration. Recent findings have established that collagen alpha-1 is involved in osteogenesis imperfecta phenotype in cattle but deep information about other members of this large family is not available so far. So with a view to finding a new edge and attempt to figure out a correlation among the well attributed Bovine alpha-1 collagen sequences are executed and analyzed. To do so, comparative analysis among the 28 members of collagen family has been carried out using Computational tools. Consequently, based on the physico-chemical, secondary structural, functional and phylogenetic classifications, we have selected collagen 12, 14 and 20 as targets for pathological conditions. These proteins belong to the FACIT family and significantly showed low glycine and proline content, high instability and aliphatic index. Moreover, FACIT family collagens contain multiple triple helical domains and being members of the FACIT family, bovine collagen 12, 14, 20 do not form fibrils by themselves but they are associated to collagen 1 associated fibrils. These collagen molecules might be crucial candidates to detect and understand the process of matrix remodeling in diseases especially in the arena of cellular compartments.
  Bioinformation 01/2013; 9(1):42-8.
• Article: Computational model for pathway reconstruction to unravel the evolutionary significance of melanin synthesis.

  Sudha Singh, Anvita Gupta Malhotra, Ajay Pandey, Khushhali M Pandey
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  ABSTRACT: Melanogenesis is a complex multistep process of high molecular weight melanins production by hydroxylation and polymerization of polyphenols. Melanins have a wide range of applications other than being a sun - protection pigment. Melanogenesis pathway exists from prokaryotes to eukaryotes. It has evolved over years owing to the fact that the melanin pigment has different roles in diverse taxa of organisms. Melanin plays a pivotal role in the existence of certain bacteria and fungi whereas in higher organisms it is a measure of protection against the harmful radiation. We have done a detailed study on various pathways known for melanin synthesis across species. It was divulged that melanin production is not restricted to tyrosine but there are other secondary metabolites that synthesize melanin in lower organisms. Furthermore the phylogenetic study of these paths was done to understand their molecular and cellular development. It has revealed that the melanin synthesis paths have co-evolved in several groups of organisms. In this study, we also introduce a method for the comparative analysis of a metabolic pathway to study its evolution based on similarity between enzymatic reactions.
  Bioinformation 01/2013; 9(2):94-100.
• Article: Genetic diversity and species pattern of Trichoderma and Hypocrea in Manipur using in silico analysis.

  Thongram Kamala, Sarangthem Indira Devi, Gourshyam Thingnam, Bharat Gopalrao Somkuwar
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  ABSTRACT: We investigated the occurrence and genetic diversity of Trichoderma and Hypocrea in Manipur which lies in the Indo-Burma biodiversity hot spot region. 65 Trichoderma isolates were identified at species level by morphological as well as sequence based analysis of the internal transcribed spacer region 1 and 4. Altogether 22 different species of Trichoderma and Hypocrea were found, of which Trichoderma harzianum represent the dominant species. Phylogenetic analysis reveals a clear cut distinction of strains isolated from various collection sites which further hints the need for detail study of Trichoderma on molecular level.
  Bioinformation 01/2013; 9(2):106-11.
• Article: BIRS - Bioterrorism Information Retrieval System.

  Ashish Kumar Tewari, Rashi, Gulshan Wadhwa, Sanjeev Kumar Sharma, Chakresh Kumar Jain
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  ABSTRACT: Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. AVAILABILITY: The database is freely available at http://www.bioterrorism.biowaves.org.
  Bioinformation 01/2013; 9(2):112-5.
• Article: Sequence and structural characterization of Trx-Grx type of monothiol glutaredoxins from Ashbya gossypii.

  Saurabh Yadav, Pragati Kumari, Hemant Ritturaj Kushwaha
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  ABSTRACT: Glutaredoxins are enzymatic antioxidants which are small, ubiquitous, glutathione dependent and essentially classified under thioredoxin-fold superfamily. Glutaredoxins are classified into two types: dithiol and monothiol. Monothiol glutaredoxins which carry the signature "CGFS" as a redox active motif is known for its role in oxidative stress, inside the cell. In the present analysis, the 138 amino acid long monothiol glutaredoxin, AgGRX1 from Ashbya gossypii was identified and has been used for the analysis. The multiple sequence alignment of the AgGRX1 protein sequence revealed the characteristic motif of typical monothiol glutaredoxin as observed in various other organisms. The proposed structure of the AgGRX1 protein was used to analyze signature folds related to the thioredoxin superfamily. Further, the study highlighted the structural features pertaining to the complex mechanism of glutathione docking and interacting residues.
  Bioinformation 01/2013; 9(5):243-9.
• Article: Sequence analysis and phylogenetic study of some toxin proteins of snakes and related non-toxin proteins of chordates.

  Subhamay Panda, Goutam Chandra
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  ABSTRACT: Snakes are equipped with their venomic armory to tackle different prey and predators in adverse natural world. The venomic composition of snakes is a mix of biologically active proteins and polypeptides. Among different components snake venom cytotoxins and short neurotoxin are non-enzymatic polypeptide candidates with in the venom. These two components structurally resembled to three-finger protein superfamily specific scaffold. Different non-toxin family members of three-finger protein superfamily are involved in different biological roles. In the present study we analyzed the snake venom cytotoxins, short neurotoxins and related non-toxin proteins of different chordates in terms of amino acid sequence level diversification profile, polarity profile of amino acid sequences, conserved pattern of amino acids and phylogenetic relationship of these toxin and nontoxin protein sequences. Sequence alignment analysis demonstrates the polarity specific molecular enrichment strategy for better system adaptivity. Occurrence of amino acid substitution is high in number in toxin sequences. In non-toxin body proteins there are less amino acid substitutions. With the help of conserved residues these proteins maintain the three-finger protein scaffold. Due to system specific adaptation toxin and non-toxin proteins exhibit a varied type of amino acid residue distribution in sequence stretch. Understanding of Natural invention scheme (recruitment of venom proteins from normal body proteins) may help us to develop futuristic engineered bio-molecules with remedial properties.
  Bioinformation 01/2013; 9(5):259-66.