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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...

Improving Translational Accuracy

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Updated: Apr 30, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

An Accurate Scalable Template-based Alignment Algorithm.

David P Gardner¹, Weijia Xu², Daniel P Miranker³

¹Institute for Cellular and Molecular Biology The University of Texas at Austin Austin, TX, USA dpgardn@utexas.edu.

Proceedings. IEEE International Conference on Bioinformatics and Biomedicine

|April 29, 2014

Summary

This summary is machine-generated.

CRWAlign accurately and quickly aligns RNA sequences by analyzing sequence conservation patterns. This new method, utilizing the rCAD database, improves upon existing RNA alignment tools.

Keywords:

RNA sequence alignment comparative analysis phylogenetic-based alignment template-based alignment

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Last Updated: Apr 30, 2026

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Large-area Scanning Probe Nanolithography Facilitated by Automated Alignment and Its Application to Substrate Fabrication for Cell Culture Studies

Large-area Scanning Probe Nanolithography Facilitated by Automated Alignment and Its Application to Substrate Fabrication for Cell Culture Studies

Published on: June 12, 2018

Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

The increasing volume of nucleic acid sequence data necessitates efficient alignment methods.
RNA sequence evolution is shaped by structural and functional constraints, reflected in conserved patterns.
Existing template-based alignment programs leverage sequence conservation but may not capture all nuances.

Purpose of the Study:

To develop a novel RNA sequence alignment program, CRWAlign, that enhances accuracy and speed.
To utilize diverse information dimensions from the rCAD RNA informatics resource for improved alignment profiles.
To establish position-specific profiles incorporating sequence identity and phylogenetic composition.

Main Methods:

Developed CRWAlign, a program integrating data from the rCAD resource.
Created position-specific alignment profiles based on sequence identity and column composition across taxa.
Compared CRWAlign's performance against eight alternative alignment methods using 16S and 23S rRNA sequences.

Main Results:

CRWAlign demonstrated superior performance in both speed and accuracy compared to eight other alignment methods.
The method effectively utilized sequence identity and phylogenetic composition for robust alignment profiles.
Evaluations were conducted on diverse rRNA datasets with sequence identities ranging from 50% to 100%.

Conclusions:

CRWAlign represents a significant advancement in RNA sequence alignment technology.
The program's ability to integrate multiple data dimensions from rCAD leads to enhanced accuracy and efficiency.
A web-based server for CRWAlign is publicly accessible for broader research application.