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Related Concept Videos

Characteristics and Nomenclature of Homopolymers01:00

Characteristics and Nomenclature of Homopolymers

3.1K
Polymers that are made up of identical monomer units are called homopolymers. Only one repeating unit is involved in the construction of the homopolymer structure. For example, as depicted in Figure 1, polypropylene is a homopolymer constituted of propylene monomers. Here, the only repeating unit in the polymer chain is propylene.
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Step-Growth Polymerization: Overview01:03

Step-Growth Polymerization: Overview

3.6K
Step-growth or condensation polymerization is a stepwise reaction of bi or multifunctional monomers to form long-chain polymers. As all the monomers are reactive, most of the monomers are consumed at the early stages of the reaction to form small chains of reactive oligomers, which then combine to form long polymer chains in the late stages. Hence, the reaction has to proceed for a long time to achieve high molecular weight polymers.
Many natural and synthetic polymers are produced by...
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Polymers02:34

Polymers

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The word polymer is derived from the Greek words “poly” which means “many” and “mer” which means “parts”. Polymers are long chains of molecules composed of repeating units of smaller molecules, known as monomers. They either occur naturally, such as DNA and proteins, or can be constructed synthetically, like plastics. They have varied structural characteristics, such as linear chains, branched chains, or complex networks, that contribute to the...
36.1K
Characteristics and Nomenclature of Copolymers01:24

Characteristics and Nomenclature of Copolymers

2.6K
Copolymers are the products obtained from the polymerization of multiple monomer species. So, in a polymer chain itself, there can be multiple repeating units that come from different monomers. The process of synthesizing a polymer from different monomer species is called copolymerization. When two monomers are involved, the polymer is known as a bipolymer. Polymers with three and four monomers are termed terpolymers and quaterpolymers, respectively. Figure 1 depicts the copolymerization of...
2.6K
Molecular Weight of Step-Growth Polymers01:08

Molecular Weight of Step-Growth Polymers

2.3K
Step growth polymerization involves bi or multifunctional monomers. Bifunctional monomers react to form linear step growth polymers, whereas multifunctional monomers react to form non-linear or branched polymers.
As the step-growth polymerization involves step-wise condensation of monomers, the molecular weight also builds up eventually. Consequently, high molecular weight polymers are obtained at the late stages of the polymerization, where 99% of monomers have been consumed.
The extent of the...
2.3K
Radical Chain-Growth Polymerization: Chain Branching01:17

Radical Chain-Growth Polymerization: Chain Branching

2.0K
The skeletal structure of polymers synthesized via radical polymerization is always branched. For example, the polymerization of ethylene by radical polymerization results in a low-density grade of polyethylene with a heavily branched skeletal structure. Here, the radical site abstracts hydrogen from the growing chain, and the radical site shifts from the end (a primary carbon center) to anywhere within the growing chain (a secondary carbon center). Consequently, the part of the chain from the...
2.0K

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Updated: Aug 22, 2025

Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

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Mapping-friendly sequence reductions: Going beyond homopolymer compression.

Luc Blassel1,2, Paul Medvedev3,4,5, Rayan Chikhi1

  • 1Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France.

Iscience
|November 7, 2022
PubMed
Summary
This summary is machine-generated.

Homopolymer compression is a common method to reduce sequencing errors in long reads. New mapping-friendly sequence reductions offer improved alignment accuracy, outperforming traditional homopolymer compression.

Keywords:
Biological sciencesBiological sciences research methodologiesMolecular biologyTranscriptomics

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Sequencing errors, particularly homopolymer errors, present significant algorithmic challenges in bioinformatics.
  • Homopolymer compression is a widely used pre-processing technique to mitigate these errors in long reads, aiming to improve mapping sensitivity.

Purpose of the Study:

  • To investigate if alternative sequence transformations, beyond homopolymer compression, can enhance alignment sensitivity.
  • To introduce and evaluate a more generalized framework for sequence reduction in the context of sequence alignment.

Main Methods:

  • Developed a framework for 'mapping-friendly sequence reductions' as a generalized approach to homopolymer compression.
  • Applied these sequence reductions to both reference genomes and sequencing reads.
  • Evaluated the impact of these reductions on alignment accuracy using standard alignment algorithms.

Main Results:

  • Demonstrated that certain mapping-friendly sequence reductions significantly improve mapping accuracy compared to standard homopolymer compression.
  • Identified specific reduction strategies that outperform the conventional homopolymer compression technique.

Conclusions:

  • Mapping-friendly sequence reductions offer a more effective pre-processing strategy for long-read sequencing data than homopolymer compression.
  • This generalized framework provides a promising avenue for improving the accuracy and sensitivity of sequence alignment algorithms.