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Related Concept Videos

Genomics02:02

Genomics

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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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Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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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.
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Genomic DNA in Eukaryotes00:58

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Sanger Sequencing01:57

Sanger Sequencing

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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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Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency.

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International Journal of Genomics
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Cassandra NoSQL databases offer an effective solution for managing and storing massive genomic datasets, outperforming traditional relational databases in performance and I/O operations for bioinformatics applications.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomic Data Management

Background:

  • High-throughput sequencing generates massive datasets, posing computational challenges.
  • Efficient storage and retrieval of large-scale genomic data are critical.
  • Relational databases may not be optimal for non-conventional, large-volume data.

Purpose of the Study:

  • To evaluate the Cassandra NoSQL database for storing and managing genomic data.
  • To analyze the performance of Cassandra for persistency and I/O operations.
  • To compare Cassandra with relational databases and MongoDB for genomic data handling.

Main Methods:

  • Utilized the Cassandra NoSQL database system.
  • Performed analysis of data persistency and I/O operations using real genomic data.
  • Compared performance against a classical relational database and MongoDB.

Main Results:

  • Cassandra demonstrated effective management of large-scale genomic data.
  • Analysis of persistency and I/O operations showed promising results for Cassandra.
  • Comparative analysis highlighted potential advantages over relational and other NoSQL models.

Conclusions:

  • The Cassandra NoSQL database is a viable and potentially superior alternative for genomic data storage.
  • Cassandra offers efficient solutions for the computational challenges in bioinformatics data management.
  • Further research can explore optimized configurations for Cassandra in genomic applications.