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RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
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ResiDB: An automated database manager for sequence data.

Michaela Hendling1, Rick Conzemius1, Ivan Barišić1

  • 1Austrian Institute of Technology, Center for Health & Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210 Vienna, Austria.

Computational and Structural Biotechnology Journal
|January 26, 2021
PubMed
Summary

ResiDB is a new webtool that simplifies the creation of custom DNA sequence databases for researchers. It automates sequence curation and management, overcoming challenges in handling large datasets and antibiotic resistance genes.

Keywords:
Antibiotic resistanceAssay designDNA databaseDiagnosticsPhylogeny

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The exponential growth of DNA sequence data presents significant challenges for creating specialized databases.
  • Manually curating sequence data, especially for genes with high mutation rates like antibiotic resistance genes, is time-consuming and complex.
  • Existing tools often require users to manage hardware limitations and multiple software with disparate formats.

Purpose of the Study:

  • To introduce resiDB, a user-friendly webtool designed for efficient management of bacterial, fungal, viral, and other sequence data.
  • To automate the identification and curation of sequence clusters for custom database generation.
  • To provide researchers with integrated tools for accessing, evaluating, editing, and downloading sequence databases.

Main Methods:

  • Development of a webtool, resiDB, for automated sequence database management.
  • Implementation of algorithms for automatic identification and curation of sequence clusters.
  • Integration of visualization tools for user interaction and data manipulation.
  • Designed for diverse sequence data including whole genome shotgun data.

Main Results:

  • ResiDB successfully automates the creation of custom sequence databases from user-defined inputs.
  • The tool streamlines data retrieval, eliminating the need for manual management and multiple software.
  • Visualization tools facilitate easy access, evaluation, editing, and downloading of curated databases.
  • The webtool supports a wide range of sequence data types.

Conclusions:

  • ResiDB significantly simplifies and accelerates the process of building custom sequence databases.
  • It addresses key challenges in managing large-scale genomic data and antibiotic resistance gene information.
  • The tool empowers researchers by reducing manual effort and improving data accessibility for diagnostic assay design.