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Related Concept Videos

Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Related Experiment Video

Updated: Jun 14, 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

Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with

Shinsuke Yamada1, Osamu Gotoh, Hayato Yamana

  • 1Department of Computer Science, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan. shinsuke@yama.info.waseda.ac.jp

BMC Bioinformatics
|December 2, 2006
PubMed
Summary
This summary is machine-generated.

We developed PRIME, a novel multiple sequence alignment algorithm that achieves high accuracy without needing pairwise alignment information. This method optimizes sequence alignment for improved bioinformatics research.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is crucial in bioinformatics, but existing algorithms face challenges in accuracy and speed, especially with long insertions/deletions.
  • Current leading MSA algorithms often integrate pairwise alignment data to enhance accuracy for sequences with significant indels.

Purpose of the Study:

  • To introduce a novel group-to-group sequence alignment algorithm designed for improved accuracy and efficiency.
  • To present PRIME (Profile-based Randomized Iteration MEthod), a software implementation of the proposed algorithm.

Main Methods:

  • Developed a novel group-to-group sequence alignment algorithm utilizing a piecewise linear gap cost.
  • Implemented the algorithm in a program named PRIME.
  • Optimized the sum-of-pairs score using the PRIME algorithm.

Main Results:

  • PRIME demonstrated comparable accuracy to leading MSA programs like MAFFT, ProbCons, and T-Coffee in benchmark tests.
  • Evaluated PRIME's performance using BAliBASE 3.0 and PREFAB 4.0 datasets.
  • The algorithm successfully constructs accurate alignments, particularly for sequences with challenging indel variations.

Conclusions:

  • PRIME offers a robust solution for accurate multiple sequence alignment without reliance on external pairwise alignment data.
  • The PRIME software is publicly accessible for researchers at http://prime.cbrc.jp/.