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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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Counting is the type of measurement that is free from uncertainty, provided the number of objects being counted does not change during the process. Such measurements result in exact numbers. By counting the eggs in a carton, for instance, one can determine exactly how many eggs are there in the carton. Similarly, the numbers of defined quantities are also exact. For example, 1 foot is exactly 12 inches, 1 inch is exactly 2.54 centimeters, and 1 gram is exactly 0.001 kilograms. Quantities...
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Inertial Frames of Reference01:03

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Newton’s first law is usually considered to be a statement about reference frames. It provides a method for identifying a special type of reference frame: the inertial reference frame. In principle, we can make the net force on a body zero. If its velocity relative to a given frame is constant, then that frame is said to be inertial. So, by definition, an inertial reference frame is a reference frame where Newton's first law holds valid. Newton's first law applies to objects with...
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A reference frame accelerating or decelerating relative to an inertial frame is a non-inertial frame. To help understand this, consider what taking off in an airplane, turning a corner in a car, riding a merry-go-round, and the circular motion of a tropical cyclone all have in common. All these systems are accelerating, decelerating, or rotating relative to the Earth; hence, they all are non-inertial frames. All these systems exhibit inertial forces, which merely seem to arise from motion,...
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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Fast and memory efficient approach for mapping NGS reads to a reference genome.

Sanjeev Kumar1, Suneeta Agarwal1, Ranvijay1

  • 11 CSED, NIT Allahabad, 211004, India.

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|May 7, 2019
PubMed
Summary

A new method, WIT, efficiently aligns short DNA reads to reference genomes using less memory and comparable speed to existing tools. This advance aids next-generation sequencing data analysis for genetic variation and re-sequencing.

Keywords:
Indexingburrows wheeler transformgenomeread alignmentsuffix arraywavelet tree

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing (NGS) technologies produce millions of short DNA reads per run.
  • Aligning these reads to a reference genome is crucial for applications like genetic variation analysis and genome re-sequencing.
  • Existing alignment tools demand substantial memory for reference genome indexing, impacting efficiency.

Purpose of the Study:

  • To develop a novel, memory-efficient approach for reference genome indexing and short read alignment.
  • To improve the speed and reduce the memory footprint of next-generation sequencing data analysis.

Main Methods:

  • Proposed WIT (Wavelet-Tree Indexing) approach utilizing Burrows-Wheeler Transform (BWT) and Wavelet Tree (WT).
  • Implemented exact and approximate alignment capabilities.
  • Evaluated WIT's performance against established tools like BWA, Subread, Kart, and Minimap2.

Main Results:

  • WIT requires significantly less reference genome indexing space (0.6N) compared to existing methods (1.25N to 5N).
  • Alignment time using WIT is comparable to other leading tools despite its smaller index size.
  • WIT demonstrated superior accuracy and confidentiality compared to Minimap2.

Conclusions:

  • WIT offers a highly efficient solution for reference genome indexing and short read alignment in next-generation sequencing.
  • The method provides a valuable alternative for large-scale genomic analyses, reducing computational resource requirements.
  • Source code for WIT is publicly available for further research and application.