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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
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Genomics02:02

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Sanger Sequencing01:57

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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RACE - Rapid Amplification of cDNA Ends02:35

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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RNA-seq03:21

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. 
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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
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KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.

Mahdieh Labani1,2, Amin Beheshti2, Nigel H Lovell3,4

  • 1Biomedical Machine Learning Lab, The Graduate School of Biomedical Engineering, University of New South Wales (UNSW), Sydney, NSW 2052, Australia.

International Journal of Molecular Sciences
|November 26, 2022
PubMed
Summary
This summary is machine-generated.

KARAJ is a new Linux command-line tool that automates downloading genomic and transcriptomic data from scientific publications. It simplifies data access, saving researchers significant time and effort.

Keywords:
BioinformaticsDownloadFASTQGenomicsLinuxbiological datasequence datatranscriptomics

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Area of Science:

  • Bioinformatics
  • Genomics
  • Transcriptomics

Background:

  • Accessing and downloading large-scale genomic and transcriptomic data from scientific literature can be a complex and time-consuming process.
  • Manual data retrieval often involves navigating multiple repositories and formats, leading to inefficiencies in research workflows.

Purpose of the Study:

  • To develop KARAJ, a novel, fast, and flexible Linux command-line tool for automating the end-to-end process of querying and downloading diverse genomic and transcriptomic sequence data.
  • To streamline the acquisition of supplementary data and metadata associated with scientific publications.

Main Methods:

  • KARAJ accepts PMCIDs, publication URLs, or accession numbers as input.
  • It automates four key tasks: identifying accessible datasets, calculating download sizes, generating metadata tables, and downloading supplementary data.
  • The tool incorporates a parallel downloading framework utilizing Aspera Connect for accelerated data transfer.

Main Results:

  • KARAJ successfully automates the querying and downloading of various genomic and transcriptomic data types.
  • The tool provides essential metadata and confirms disk space adequacy before download.
  • Parallel downloading via Aspera Connect significantly reduces data acquisition time.

Conclusions:

  • KARAJ offers a robust and efficient solution for researchers needing to access genomic and transcriptomic data linked to publications.
  • The automation and parallel download features of KARAJ enhance research reproducibility and accelerate discovery by simplifying data management.