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Trends in Bioinformatics
eISSN: 2077-2254
pISSN: 1994-7941

Editor-in-Chief:  Amir Feisal Merican
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Research Article
Published on March 28, 2018
ArchaeVir: A Comprehensive Genometrics Database of Archaeal Viruses
Krishna Kumar Ojha, Swapnil Mishra and Lalit Kumar Pandey
Background and Objective: The era of high throughput sequencing technology has poured thousands of full genomes sequences in public databases. A remarkable portion of these genomic sequences belongs to the viruses of which viruses infecting archaea are least studied group. Archaeal viruses are morphologically more diverse than bacterial ones and display unique morphotypes. All sequenced archaeal viruses have DNA as their genetic material, which is double stranded in most of the cases. In this study, applied biometric method to understand the local and global feature of nucleotide distribution in all available archaeal genomes on Genbank. ArchaeVir database is dedicated to characterization of archaeal virus genomes with standardized genometrics of Z-curve and cumulative GC and AT skews. Material and Methods: All archaea viruses genomes were downloaded from NCBI. A script was written in MATLAB to calculate and plot the cumulative Z-curve and nucleotide skews. Database was created using MySQL and PHP, AJAX was used to create front end of the database. Results: Genometrics is a biometric analysis of chromosomes which is capable of identifying, at the level of whole genomes, features inherent to chromosome organization and functioning. This database also hosts the basic genomic records like genome length, GC%, total genes and proteins all sequenced viral genomes of archaea. In addition to this, two tools, one for finding the repeats and nucleotide distribution and second for plotting the geometric skew of nucleotide sequence has also been integrated with this database. Conclusion: Genometrics data of archaeal viruses available on the database could be readily accessed by the scientific community for further analysis of local and global features of viral genomes as well as for tutorial purpose.
Research Article
In silico Studies for Potential Natural Inhibitors for Isocitrate Dehydrogenase Type II of Mycobacterium tuberculosis (H37Rv)
Swapnil Mishra, Krishna Kumar Ojha, Paras Nath Pandey and Akanchha Shukla
Background and Objective: Tuberculosis is a life threatening bacterial disease caused by Mycobacterium tuberculosis (M. tuberculosis) which has affected the population of almost all parts of the world since time immemorial. Although remarkable discovery has been achieved in combating disease control and its propagation but due to emergence of resistant strain of M. tuberculosis exhaustive search for the panacea to counter the bacteria is still on. This study proposes in silico studies of 35 natural compounds against proposed drug target isocitrate dehydrogenase type II (PDBID: 5 KVU) of M. tuberculosis (H37Rv). Almost all available antitubercular drugs in the market now-a-days have some side effects. Hence, there is a strong need of some natural antitubercular compounds that can mitigate the side effects and boost up the overall health of the patients. The aim of the present study was to explore the potential novel natural inhibitor against proposed drug target, isocitrate dehydrogenase II. Materials and Methods: Crystal structure of isocitrate dehydrogenase II was obtained from PDB. All natural compounds used in this study were obtained from Pubchem database and their drug likeliness was also crosschecked. Docking studies were performed with the help of Autodock 4.0. NADP+ was used as a reference ligand to compare the docking results with natural compounds. Molecular dynamics study of the docked complex has also been performed to infer the deep insight of the various interactions and stability of the receptor-ligand docked complex. Results: Results showed that molecular docking of isocitrate dehydrogenase II of M. tuberculosis against all 35 natural multi-beneficial compounds, Amentoflavone attained the minimum binding energy, hence amentoflavone is most potential natural compound that may inhibit the proposed enzyme. The molecular dynamics study of the docked receptor ligand complex also showed good congruence to the docking result. Conclusion: Natural compounds showed good binding energies with the receptor protein isocitrate dihydogenase II and amentoflavone, a natural ligand may act as a strong anti-tubercular lead compound against M. tuberculosis.
Research Article
PremipreD: Precursor miRNA Prediction by Support Vector Machine Approach
Sasti Gopal Das, Hirak Jyoti Chakraborty and Abhijit Datta
Background and Objective: Precursor microRNA expressions vary depending on their cellular environment and a large amount of genome segments can be folded in similar pseudo precursor’s microRNA hairpins like structure. Therefore, detection of true precursor microRNA in a genome is challenging task. The computational prediction of precursor MicroRNAs first distinguishes a large amount of similar folded hairpins like structure in genome sequence as a pseudo or true precursor miRNAs. However, researchers need to be improving methods for identification of precursor MicroRNA in a genomic sequence. Materials and Methods: In this computational method, supervised machine learning approach was used as a classifier for classifying the true precursor miRNAs using sequence and secondary structure information. Results: The support vector machine (SVM) classifier achieved accuracy (Q) of 96.28% for predicting true pre-miRNAs. Here, a new precursor miRNA identification tool-PremipreD was developed which performs better in comparison to existing tools, in terms of overall performance and specificity. Conclusion: The PremipreD algorithm reduces the number of false positive prediction rate by using effective Support vector machine methods.
Research Article
Morphological and Molecular Identification of Paraorygmatobothrium floraformis in Rhizoprionodon acutus off Nellore Coast, Bay of Bengal, India
Chadamala Srinivasa Kalyan and Anu Prasanna Vankara
Background and Objective: Elasmobranchs (Sharks, skates, rays) are frequently available marine fishes which serve as an ideal host for the cestode parasites. Paraorygmatobothrium floraformis (Southwell, 1912) Ruhnke, 2011 is a cestode comprising a ubiquitous and specious genus of elasmobranch parasites. This parasite was isolated from the spiral intestine of commercially available elasmobranch fish, Rhizopriondon acutus of the Nellore coast, Bay of Bengal. The main objective of this work is to evaluate the morphological criteria, molecular characterization of Paraorygmatobothrium floraformis using the 28S ribosomal DNA and to determine the phylogenetic position of this species with bioinformatics tools like BLAST and Mega 6. Materials and Methods: The present study is restricted to Nellore Coast, which has a coastline of 169 km. The milk shark, Rhizopriondon acutus was collected from the local fisherman and the nearby Coastal areas of Nellore to examine the cestodes from their spiral intestines. They were preserved in FAA (Formalin-10 mL, Alcohol-85 mL and Acetic acid-5 mL) for further morphological analysis. Also, few parasites were fixed in 95% molecular grade ethanol and placed at low temperature of -20̊C for further molecular analysis. Results: The morphological data was taken from the whole mounts. However, the obtained gene sequences of the cestode parasite were submitted to the Genbank. The gene sequence of the parasite was compared with the available gene sequences of other cestode parasite from other elasmobranchs in the Genbank. The pairwise alignment of gene sequences showed 80% similarity with the order Tetraphyllidea and 5-10% mismatches with the sequences of Phyllobothriidea family. Also, the host, Rhizoprionodon acutus and Nellore coast serve as new host record and locality records for Paraorygmatobothrium floraformis (Southwell, 1912) Ruhnke, 2011. Conclusion: Species identification is one of the major difficulties in marine fish parasites. Ribosomal DNA has been widely used for taxonomic studies. The study presents a small molecular phylogenetic analysis of the elasmobranch tapeworms of family phyllobothridea and order Tetraphyllidea. These types of analyses can reveal the relationship between different orders, families and species of the cestode parasites from the marine environment.

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