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Updated: Jun 12, 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

GUIDANCE: a web server for assessing alignment confidence scores.

Osnat Penn¹, Eyal Privman, Haim Ashkenazy

¹Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

Nucleic Acids Research

|May 26, 2010

Summary

This summary is machine-generated.

The GUIDANCE web-server identifies unreliable regions in multiple sequence alignments (MSA). It helps researchers improve sequence analysis accuracy by highlighting and removing problematic alignment sections.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Accurate multiple sequence alignment (MSA) is fundamental for comparative sequence analysis.
Identifying unreliable alignment regions is crucial for downstream analyses.

Purpose of the Study:

To present the GUIDANCE web-server, a tool for identifying unreliable regions in MSAs.
To provide a user-friendly platform for assessing alignment accuracy.

Main Methods:

The GUIDANCE web-server accepts unaligned sequences and performs MSA using user-selected algorithms (ClustalW, MAFFT, PRANK).
It employs two algorithms (heads-or-tails and GUIDANCE method) to evaluate confidence scores for columns, residues, and sequences.
Confidence scores are visualized using a color-coding scheme.

Main Results:

The server identifies unreliable alignment columns and sequences based on confidence scores.
These unreliable regions can be automatically removed for improved downstream analyses.
The tool supports nucleotide, protein, and codon sequences.

Conclusions:

The GUIDANCE web-server offers a robust solution for evaluating MSA accuracy.
It enhances the reliability of comparative sequence analysis by identifying and facilitating the removal of uncertain alignment regions.