+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

A novel approach to local reliability of sequence alignments



A novel approach to local reliability of sequence alignments



Bioinformatics 18(6): 847-854



Motivation: The pairwise alignment of biological sequences obtained from an algorithm will in general contain both correct and incorrect parts. Hence, to allow for a valid interpretation of the alignment, the local trustworthiness of the alignment has to be quantified. Results: We present a novel approach that attributes a reliability index to every pair of residues, including gapped regions, in the optimal alignment of two protein sequences. The method is based on a fuzzy recast of the dynamic programming algorithm for sequence alignment in terms of mean field annealing. An extensive evaluation with structural reference alignments not only shows that the probability for a pair of residues to be correctly aligned grows consistently with increasing reliability index, but moreover demonstrates that the value of the reliability index can directly be translated into an estimate of the probability for a correct alignment.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 010081037

Download citation: RISBibTeXText

PMID: 12075020

DOI: 10.1093/bioinformatics/18.6.847


Related references

Local reliability measures from sets of co-optimal multiple sequence alignments. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2008: 15-24, 2008

Estimation and reliability of molecular sequence alignments. Biometrics 51(1): 100-113, 1995

Heads or tails: a simple reliability check for multiple sequence alignments. Molecular Biology and Evolution 24(6): 1380-1383, 2007

Advantages of using multiple sequence alignments over pairwise alignments when sequence similarity is low. Abstracts of Papers American Chemical Society 203(1-3): BIOL60, 1992

Local sequence alignments with monotonic gap penalties. Bioinformatics 15(6): 455-462, 1999

Sampling rare events: statistics of local sequence alignments. Physical Review. E Statistical Nonlinear and Soft Matter Physics 65(5 Pt 2): 056102, 2002

Approximate p-values for local sequence alignments: numerical studies. Journal of Computational Biology 8(5): 549-556, 2001

A fast algorithm for determining the best combination of local alignments to a query sequence. Bmc Bioinformatics 5: 62-62, 2004

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements. Algorithms for Molecular Biology 12: 22, 2017

Misleading local sequence alignments: implications for comparative protein modelling. Protein Engineering 11(8): 627-630, 1998

Accurate formula for P-values of gapped local sequence and profile alignments. Journal of Molecular Biology 300(3): 649-659, 2000

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research 34(Web Server Issue): W609, 2006

Building multiple sequence alignments with a flavor of HSSP alignments. Genetics and Molecular Research 5(1): 127-137, 2006

An information theoretic approach to macromolecular modeling: I. Sequence alignments. Biophysical Journal 89(5): 2998-3007, 2005

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. Journal of Molecular Biology 264(4): 823-838, 1996