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A novel approach to local reliability of sequence alignments
Maximilian Schlosshauer1, Mattias Ohlsson
1Complex Systems Division, Department of Theoretical Physics, University of Lund, Sölvegatan 14A, Sweden.
Bioinformatics (Oxford, England)
|June 21, 2002
Summary
This study introduces a reliability index for protein sequence alignments, quantifying local trustworthiness. Higher reliability scores directly correlate with a greater probability of correct residue pairings in alignments.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Pairwise sequence alignment algorithms generate alignments with both accurate and inaccurate residue pairings.
- Quantifying the local trustworthiness of alignments is crucial for valid biological interpretation.
Purpose of the Study:
- To develop a novel method for assessing the reliability of pairwise protein sequence alignments.
- To provide a quantitative measure for the trustworthiness of aligned residue pairs, including gaps.
Main Methods:
- A fuzzy dynamic programming approach based on mean field annealing was employed.
- A reliability index was assigned to each pair of residues within the optimal alignment.
Main Results:
- The probability of correct residue alignment increases with the reliability index.
- The reliability index directly estimates the probability of a correct alignment for residue pairs.
Conclusions:
- The proposed reliability index offers a robust way to evaluate the quality of pairwise protein sequence alignments.
- This method enhances the interpretation of sequence alignments in biological research.