Estimation and Reliability of Molecular Sequence Alignments

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Estimation and reliability of molecular sequence alignments.

The problem of estimating the relatedness of a pair of biological sequences is addressed. A stochastic model of sequence evolution is described that allows insertion and deletion as well as replacement of amino acid residues (or substitution of nucleotides) over time. An expectation-maximization (EM) algorithm that obtains maximum likelihood estimates of the model parameters is introduced. The ...

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Empirical estimation of the reliability of ribosomal RNA alignments

MOTIVATION The automatic alignment of rRNA sequences can reproduce manual expert alignments with high, but not perfect, fidelity. We examine the use of empirical methods for the identification of regions of an alignment of a new sequence with an existing large alignment which can confidently be predicted to be correctly aligned. RESULTS We show how to use a simple jack-knife procedure to deri...

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A novel approach to local reliability of sequence alignments

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, i...

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Quality estimation of multiple sequence alignments by Bayesian hypothesis testing

UNLABELLED In this work we present a web-based tool for estimating multiple alignment quality using Bayesian hypothesis testing. The proposed method is very simple, easily implemented and not time consuming with a linear complexity. We evaluated method against a series of different alignments (a set of random and biologically derived alignments) and compared the results with tools based on clas...

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ژورنال

عنوان ژورنال: Biometrics

سال: 1995

ISSN: 0006-341X

DOI: 10.2307/2533318