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Related Concept Videos

Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Related Experiment Video

Updated: Jun 6, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Reticular alignment: a progressive corner-cutting method for multiple sequence alignment.

Adrienn Szabó1, Adám Novák, István Miklós

  • 1Computer and Automation Research Institute, Hungarian Academy of Sciences, Lágymányosi u 11, 1111 Budapest, Hungary.

BMC Bioinformatics
|November 25, 2010
PubMed
Summary

Reticular Alignment improves multiple sequence alignment by searching a network of optimal and suboptimal alignments. This method achieves higher accuracy when combined with sophisticated scoring schemes, outperforming established tools like ClustalW.

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Area of Science:

  • Bioinformatics
  • Computational Biology

Background:

  • Introduces Reticular Alignment, a novel progressive corner-cutting method for multiple sequence alignment.
  • Differs from prior methods by defining optimal and suboptimal alignments at each progressive step, stored in an efficient network structure.
  • Features a threshold parameter controlling network size and search depth within the alignment space.

Purpose of the Study:

  • To present and evaluate the Reticular Alignment method for enhanced multiple sequence alignment accuracy.
  • To demonstrate the method's performance against existing alignment tools.

Main Methods:

  • Implementation in Java and testing on the BAliBASE database.
  • Utilizes a network representation to store and efficiently manage multiple alignment possibilities.
  • Employs a threshold parameter to adjust the search depth and network size.

Main Results:

  • Reticular Alignment, with a simple scoring scheme and increased threshold, outperforms ClustalW.
  • Combined with sophisticated scoring schemes, it surpasses FSA and, in some metrics, MAFFT.
  • The program is publicly available at http://phylogeny-cafe.elte.hu/RetAlign/.

Conclusions:

  • Reticular alignment offers an efficient strategy for achieving accurate multiple sequence alignments.
  • Optimal accuracy is realized through the integration of this search strategy with advanced scoring schemes.