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Related Concept Videos

Sequences01:29

Sequences

283
Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
283
Arithmetic Sequences01:30

Arithmetic Sequences

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An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the...
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Geometric Sequences01:30

Geometric Sequences

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In systems where values diminish by a constant proportion at each stage, the resulting sequence follows a geometric structure. Each new value in the sequence is obtained by applying a fixed multiplier to the preceding term. This regular, proportional decline type is often used to represent processes involving gradual loss, such as energy dissipation or reduction in amplitude over time.When analyzing the total effect of such a process across unlimited iterations, the series of values is referred...
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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No description available
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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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Sequence database versioning for command line and Galaxy bioinformatics servers.

Damion M Dooley1, Aaron J Petkau2, Gary Van Domselaar2

  • 1Department of Pathology, University of British Columbia, Vancouver, BC, Canada.

Bioinformatics (Oxford, England)
|December 15, 2015
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Summary
This summary is machine-generated.

Reproducing bioinformatics results requires versioned sequence databases. A new system combines Kipper software, BioMAJ, and Galaxy to efficiently manage and access multiple database versions for reproducible research.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Management

Background:

  • Reproducing bioinformatics results necessitates version control for reference sequence databases.
  • Managing multiple database versions is challenging due to storage constraints and inconsistencies across resources.

Purpose of the Study:

  • To develop an integrated solution for efficient versioning and accessibility of bioinformatics sequence databases.
  • To enable reproducible research by simplifying the management of database versions for bioinformatics pipelines.

Main Methods:

  • Integration of Kipper (key-value large file versioning system), BioMAJ (database downloader), and Galaxy (web-based platform).
  • Kipper's data store format allows efficient storage of multiple database versions, minimizing storage overhead.

Main Results:

  • A combined software package enables command-line and Galaxy users to access specific database versions.
  • The Kipper data store format efficiently stores multiple versions, with file sizes only slightly larger than the latest version.

Conclusions:

  • The developed system provides an end-to-end solution for managing and accessing versioned sequence databases.
  • This approach facilitates reproducible bioinformatics analyses and simplifies database management for researchers.