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Not Available: In this paper, we describe small area estimation (SAE) under a spatial dependent random effects model by combining data from two independent surveys. The spatial dependence is introduced using simultaneous autoregressive (SAR) structure in the random area effects part of the model. We use data from two independent surveys. The first survey, small in sample size, collects both variable of interest as well as auxiliary variables and the second survey, relatively larger in sample size, has some auxiliary variables common to the first survey. Our empirical results, based on simulation studies, show that proposed SAE method using the data from two surveys is efficient as compared to the one based on data from single survey. Use of spatial information further enhances the efficiency of the proposed estimato

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Not AvailableCurrent de-novo assemblers are unable to effectively use the long-read sequencing data generated by present single-molecule sequencing technologies primarily because of the considerable error rate. In this project, both long and short reads have been required for efficient assembly results. The error correction on long reads were performed by aligning short reads over long reads to get reduced errors on the long reads and use them for assembly. Our approach exploits this technology by complementing it with shorter, high-identity sequences resulting in long, accurate transcripts and improved assemblies. The result of our hybrid approach is higher quality assemblies with fewer errors and gaps, which will drive down the expensive cost of genome finishing and enable more accurate downstream analyses. High-quality assemblies are critical for all aspects of genomics, especially genome annotation and comparative genomics. It is clear that higher-quality assemblies, with long unbroken contigs, will have a positive impact on a wide range of disciplines.This way, it is noticed that high error rates do not become a barrier to genome assembly. Higherror, long reads can be efficiently assembled in combination with complementary short-reads to produce assemblies not possible with any prior technology, bringing us one step closer to the goal of “one chromosome, one contig.” The rapid turnaround time possible with PacBio and other technologies, such as Ion Torrent, can make it possible to produce high-quality genome assemblies at a fraction of the time once required.Many tools in bioinformatics run on parallelized computational infrastructure for getting results in a comparatively less time because of heavy computational algorithms or job sizes involved. In this work, the parallelized tools installed on supercomputing infrastructure were utilized for faster results. The genome assembly is carried out in a pipeline form and running tools on HPC environment. This study was undertaken with the objectives to create a web-based software for various components of assembly namely – pre-processing, alignment for error correction, long read assembly and scaffolding. The software has been developed using JSP, Java, HTML and CSS. This software does a series of computations for all the steps involved. These computations are done on ASHOKA supercomputing system to get the faster results. The results are shown to the user on the browser which can also be downloaded to the client’s local hard disk.Not Availabl

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Not AvailableAssembly of genome sequences of a microbial community is computationally challenging and complex than its single genome counterparts. Keeping in view the volume, diversity and varied abundance of different microbes, number of metagenome assemblers have been developed addressing specific associated computational issues mainly following De Bruijn Graph (DBG) and Overlap Layout Consensus (OLC) approaches. It is very pertinent to understand different computational approaches and issues of metagenomic assembly to further improve them with respect to time and computational resource requirements. Therefore, the main objective of this article is to discuss various etagenomics assemblers with respect to their development addressing major computational issues. Initially the computational perspective of single genome assemblers based on OLC and DBG graph construction approaches was described. This is followed by review of metagenomic assemblers with respect to the algorithm implemented for addressing issues in metagenome assembly. Further, performance of some of the popular metagenome assemblers were empirically evaluated with respect to their run time and memory requirements by taking diversified benchmark metagenomics data at ICAR-IASRI, New Delhi in 2019. It was concluded that performance of assemblers varied considerably on these datasets and there is further need to make an effort to develop new tools or to modify the existing ones using efficient algorithms and data structures.Not Availabl

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Not AvailablePigeon pea is avital food legume crop grown in India. Pigeon pea is consumed as green pea, whole grain or split pea. Many studies have been under taken by researchers for the analysis of whole genome sequence of pigeon pea. Also, post transcriptional gene regulation has emerged as an important technology for crop sciences. The discoveries of miRNAs in plants and the growing evidence of their involvement in a variety of functional roles have produced a great deal of excitement in plant biology. Approaches developed for identification of miRNAs are in-vitro, in-silico and combination of both these. This study was undertaken to identify the miRNAs in pigeon pea using computational methods. Eleven miRNAs were identified using this method. This study will help in improved understanding of molecular mechanisms of miRNA and development of novel and more precise techniques for better understanding of post-transcriptional gene silencing in pigeon pea.Not Availabl

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Not AvailableA trial was conducted to assess genetic parameters and diversity in physic nut (Jatropha curcas L.). Data were collected on ten biometric traits during year 2007 to 2008 and 2008 to 2009. Genotype Indira Gandhi Agricultural University (IGAU)-Raipur ranked first for seed yield (0.269, 0.492 kg/plant) in year 2007 to 2008 and 2008 to 2009, respectively. In 2007 to 2008, dry fruit yield/plant accounted highest phenotypic coefficient of variation (PCV) (40.27%) while seed yield/plant recorded highest genotypic coefficient of variation (GCV) (26.36%) in comparison to other traits. In contrast, in 2008 to 2009, seed yield/plant had highest PCV (45.88%) as well as GCV (34.27%). High estimates of heritabilities (h2) coupled with high genetic gains (GA) were registered for number of fruit clusters/plant, seed yield/plant and dry fruit yield/plant for both years which implies that direct selection would be effective for improvement of these traits. The maximum Euclidean distance of 11.21% was registered between IGAU Raipur and Lower Sowan. Non-hierarchical Euclidean analysis grouped forty six genotypes of J. curcas into five non-overlapping clusters. The maximum (7.723) inter-cluster distance was noticed between cluster NC-I and NC-IV whereas, minimum (2.747) inter-cluster distances was in between NC-I and NC-V. Based on three methods of clustering namely; hierarchical clustering, non-hierarchical clustering and metroglyph clustering, pooled clusters were formed which were found to be effective in selection of genotypes forhybridization. (12) (PDF) Variability and genetic diversity assessment in physic nut (Jatropha curcas L.). Available from: https://www.researchgate.net/publication/303178007_Variability_and_genetic_diversity_assessment_in_physic_nut_Jatropha_curcas_L [accessed Nov 27 2018].Not Availabl

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Not AvailableThe application of novel and modern techniques in genetic engineering and genomics has resulted in information explosion in genomics. Three major genome databases under International Nucleotide Sequence Database collaboration NCBI, DDBJ and EMBL have been providing a convenient platform for submission of sequences which they share among themselves. Many institutes in India under Indian Council of Agricultural Research have scientists working on biotechnology and bioinformatics research. The various studies conducted by them, generate massive data related to biological information of plants, animals, insects, microbes and fisheries. These scientists are dependent on NCBI, EMBL, DDBJ and other portals for their sequence submissions, analysis and other data mining tasks. Due to various limitations imposed on these sites and the poor connectivity problem prevents them to conduct their studies on these open domain databases. The valued information generated by them needs to be shared by the scientific communities to eliminate the duplication of efforts and expedite their knowledge extended towards new findings. A secured common submission portal system with user-friendly interfaces, integrated help and error checking facilities has been developed in such a way that the database at the backend consists of a union of the items available on the above mentioned databases. Standard database management concepts have been employed for their systematic storage management. Extensive hardware resources in the form of high performance computing facility are being installed for deployment of this portal.Not Availabl

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Not AvailableHalophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: http://webapp.cabgrid.res.in/protein/Not Availabl

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Not AvailableLate blight is a serious disease in potato caused by Phytophthora infestans. To date only few miRNA have been discovered which are related to late blight disease of potato during host pathogen interaction. Recent studies showed that miRNA, an important gene expression regulator, plays a very important role in host-pathogen interaction by silencing genes either by destructing or blocking of translation of mRNA.Not Availabl

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Not AvailableBackground: Binning of metagenomic reads is an active area of research, and many unsupervised machine learning-based techniques have been used for taxonomic independent binning of metagenomic reads. Objective: It is important to find the optimum number of the cluster as well as develop an efficient pipeline for deciphering the complexity of the microbial genome. Methods: Applying unsupervised clustering techniques for binning requires finding the optimal number of clusters beforehand and is observed to be a difficult task. This paper describes a novel method, MetaConClust, using coverage information for grouping of contigs and automatically finding the optimal number of clusters for binning of metagenomics data using a consensus-based clustering approach. The coverage of contigs in a metagenomics sample has been observed to be directly proportional to the abundance of species in the sample and is used for grouping of data in the first phase by MetaConClust. The Partitioning Around Medoid (PAM) method is used for clustering in the second phase for generating bins with the initial number of clusters determined automatically through a consensus- based method. Results: Finally, the quality of the obtained bins is tested using silhouette index, rand Index, recall, precision, and accuracy. Performance of MetaConClust is compared with recent methods and tools using benchmarked low complexity simulated and real metagenomic datasets and is found better for unsupervised and comparable for hybrid methods.Not Availabl

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Not AvailableCereals are the most important food crops and are considered key contributors to global food security. Loss due to abiotic stresses in cereal crops is limiting potential productivity in a significant manner. The primary reasons for abiotic stresses are abrupt temperature, variable rainfall, and declining nutrient status of the soil. Varietal development is the key to sustaining productivity under influence of multiple abiotic stresses and must be studied in context with genomics and molecular breeding. Recently, advances in a plethora of Next Generation Sequencing (NGS) based methods have accelerated the enormous genomic data generation associated with stress-induced transcripts such as microarray, RNAseq, Expressed Sequenced Tag (ESTs), etc. Many databases related to microarray and RNA-seq based transcripts have been developed and profusely utilized. However, an abundant amount of transcripts related to abiotic stresses in various cereal crops arising from EST technology are available but still remain underutilized in absence of a consolidated database. In this study, an attempt has been made with a primary goal to integrate, analyse, and characterise the available resources of ESTs responsive to abiotic stresses in major cereals. The developed CerealESTdb presents a customisable search in two different ways in the form of searchable content for easy access and potential use. This database comprises ESTs from four major cereal crops, namely rice (Oryza sativa L.), wheat (Triticum aestivum L.), sorghum (Sorghum bicolour L.), and maize (Zea mays L.), under a set of abiotic stresses. The current statistics of this cohesive database consists of 55,826 assembled EST sequences, 51,791 predicted genes models, and their 254,609 gene ontology terms including extensive information on 1,746 associated metabolic pathways. We anticipate that developed CerealESTdb will be helpful in deciphering the knowledge of complex biological phenomena under abiotic stresses to accelerate the molecular breeding programs towards the development of crop cultivars resilient to abiotic stresses. The CerealESTdb is publically available with the URL http://cabgrid.res.in/CerealESTDb.Not Availabl