Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Jiménez-López, José Carlos; Gachomo, Emma W.; Sharma, Sweta; Kotchoni, Simeon O.

doi:10.4236/ajmb.2013.32016

Cited by 9 publications

(6 citation statements)

References 92 publications

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“…The sequences of seven available isoforms of NLL β-conglutin protein were retrieved from the NCBI database (accession number F5B8V9, F5B8W0–F5B8W5 corresponding to β1 to β7). A multiple sequence alignment and subsequent analysis was performed using ClustalW software (), based on Blosum62 matrix (BLOck SUbstitution Matrix) [24], and viewed using the Jalview viewer 2.2 (). The Bioedit v 7.0.5.3 () software was used to calculate the sequence identity matrices.…”

Section: Methodsmentioning

confidence: 99%

Narrow-Leafed Lupin Main Allergen β-Conglutin (Lup an 1) Detection and Quantification Assessment in Natural and Processed Foods

Lima-Cabello

Alché

Jiménez-López

2019

Foods

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The increasing prevalence of lupin allergy as a consequence to the functional characteristics of a growing number of sweet lupin-derived foods consumption makes the imperious necessity to develop analytical tools for the detection of allergen proteins in foodstuffs. The current study developed a new highly specific, sensitive and accurate ELISA method to detect, identify and quantify the lupin main allergen β-conglutin (Lup an 1) protein in natural and processed food. The implementation of accurate standards made with recombinant conglutin β1, and an anti-Lup an 1 antibody made from a synthetic peptide commonly shared among β-conglutin isoforms from sweet lupin species was able to detect up to 8.1250 ± 0.1701 ng (0.0406 ± 0.0009 ppm) of Lup an 1. This identified even lupin traces present in food samples which might elicit allergic reactions in sensitized consumers, such as β-conglutin proteins detection and quantification in processed (roasted, fermented, boiled, cooked, pickled, toasted, pasteurized) food, while avoiding cross-reactivity (false positive) with other legumes as peanut, chickpea, lentils, faba bean, and cereals. This study demonstrated that this new ELISA method constitutes a highly sensitive and reliable molecular tool able to detect, identify and quantify Lup an 1. This contributes to a more efficient management of allergens by the food industry, the regulatory agencies and clinicians, thus helping to keep the health safety of the consumers.

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Section: Methodsmentioning

confidence: 99%

Narrow-Leafed Lupin Main Allergen β-Conglutin (Lup an 1) Detection and Quantification Assessment in Natural and Processed Foods

Lima-Cabello

Alché

Jiménez-López

2019

Foods

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“…As genomics data is growing with the advances in high-throughput sequencing technologies, the size of raw data generated also increases. In order to improve the ease of access to NGS datasets, we have developed GenoVault with a user friendly interface for the retrieval of data for the scientific community [26]. GenoVault is a private cloud-based central repository for storing and retrieval of genomic data generated by various research groups.…”

Section: Genovault Private Cloud Repositorymentioning

confidence: 99%

GenoVault: A Cloud Based Genomics Repository

Jain

Saxena

Hesarur

et al. 2020

Preprint

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GenoVault is a cloud-based repository for handling Next Generation Sequencing (NGS) data. It is developed using OpenStack based private cloud with various services like keystone for authentication, cinder for block storage, neutron for networking and nova for managing compute instances for the Cloud. GenoVault uses object-based storage, which enables data to be stored as objects instead of files or blocks for faster retrieval from different distributed object nodes. Along with a web-based interface JavaFX-based desktop client has also been developed to meet the requirements of large file uploads ( > 5 GB) that is usually seen in NGS datasets. Users can store as many as one million files in their respective object based storage areas and the metadata provided by the user during file uploads is used for querying the database. GenoVault repository is designed taking into account future needs and hence can scale both vertically and horizontally without any need for modification in the design. Users have an option to make the data shareable to the public or restrict the access as private. Data security is ensured as every container is a separate entity in object-based storage architecture also supported by secured file transfer protocol during data upload and download. The data is uploaded by the user in their individual containers that include raw read files (fastq), processed alignment files (bam, sam, bed) and output of variation detection (vcf). GenoVault architecture allows verification of the data in terms of integrity and authentication before making it available to collaborators as per user permissions. GenoVault is useful for maintaining the organization wide NGS data generated by experiments in various labs which is not yet published and submitted to public repositories like NCBI. GenoVault also provides support to share NGS data among the collaborating institutions. GenoVault can thus manage vast volumes of NGS data on any OpenStack-based private cloud.

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“…Nowadays, the development of high throughput methodologies and advanced genomics are leveraging the genome-wide characterization of many different species [ 1 ]. Next Generation sequencing (NGS) technologies are strongly supporting this progress, being extensively exploited for both genome sequencing and gene expression investigations.…”

Section: Introductionmentioning

confidence: 99%

NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome

Bostan

Chiusano

2015

BMC Plant Biol

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BackgroundNext Generation Sequencing technologies (NGS) unexpectedly pushed forward the capability of solving genome organization and of widely depicting gene expression. However, although the flourishing of tools to process the NGS data, versatile and user-friendly computational environments for integrative and comparative analyses of the results from the increasing amount of collections are still required.The gene expression of tomato tissues has been widely investigated in the years, thanks to both EST sequencing and different microarray platforms. However, the resulting collections are heterogeneous in terms of experimental approaches, genotypes and conditions, making the data far from representing a gene expression atlas for the species. Therefore, the recent release of NGS transcriptome collections from several tissues and stages from physiological conditions for specific tomato genotypes provides a relevant resource to be appropriately exploited to address key questions on gene expression patterns, such as those related to fruit ripening and development in tomato. The organization of the results from the processed collections in web accessible environments, enriched with tools for their exploration, may represent a precious opportunity for the scientific research in tomato and a reference example for similar efforts.DescriptionHere we present the architecture and the facilities of NexGenEx-, a web based platform that offers processed NGS transcriptome collections and enables immediate analyses of the results. The platform allows gene expression investigations, profiling and comparisons, and exploits different resources.Specifically, we present here the platform partition NexGenEx-Tom, dedicated to the organization of results from tomato NGS based transcriptomes.ConclusionIn the current version, NexGenEx-Tom includes processed and normalized NGS expression data from three collections covering several tissue/stages from different genotypes. Beyond providing a user-friendly interface, the platform was designed with the aim to easily be expanded to include other NGS based transcriptome collections. It can also integrate different genome releases, possibly from different cultivars or genotypes, but even from different species. The platform is proposed as an example effort in tomato, and is described as a profitable approach for the exploitation of these challenging and precious datasets.

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Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Cited by 9 publications

References 92 publications

Narrow-Leafed Lupin Main Allergen β-Conglutin (Lup an 1) Detection and Quantification Assessment in Natural and Processed Foods

Narrow-Leafed Lupin Main Allergen β-Conglutin (Lup an 1) Detection and Quantification Assessment in Natural and Processed Foods

GenoVault: A Cloud Based Genomics Repository

NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome

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