MOTIVATION Sequence alignment is the problem of finding the optimal character-by-character correspondence between two sequences. It can be readily solved in O(n2) time and O(n2) space on a serial machine, or in O(n) time with O(n) space per O(n) processing elements on a parallel machine. Hirschberg's divide-and-conquer approach for finding the single best path reduces space use by a factor of n...

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This paper presents a dynamic programming algorithm for aligning two sequences when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computations time and O(M+N) space, when F is the area of the feasible region and M and N are the sequence lengths. The result extends to concave ...

Protein sequence alignment is the task of identifying evolutionarily or structurally related positions in a collection of amino acid sequences. Although the protein alignment problem has been studied for several decades, many recent studies have demonstrated considerable progress in improving the accuracy or scalability of multiple and pairwise alignment tools, or in expanding the scope of task...

This work proposes a new approach to the alignment of multiple sequences. We take profit from some results on Grammatical Inference that allow us to build iteratively an abstract machine that considers in each inference step an increasing amount of sequences. The obtained machine compile the common features of the sequences, and can be used to align these sequences. This method improves the tim...

We develop a statistical theory of probabilistic sequence alignments derived from a 'thermodynamic' partition function at finite temperature. Such alignments are a generalization of those obtained from information-theoretic approaches. Finite-temperature statistics can be used to characterize the significance of an alignment and the reliability of its single element pairs.

log g i,j f(j) . For large n, the resulting PAM matrices often allow one to find related proteins even when there are practically no matches in the alignment. In this case, the underlying nucleotide sequences are so diverged that their comparison usually fails to find any statistically significant similarities. For example, the similarity between the cancer-causing ν-sis oncogene and the growth...

Sequence alignments are becoming more important with the increase of nucleic acid data. Fitch and Smith have recently given an example where multiple insertion/deletions (rather than a series of adjacent single insertion/deletions) are necessary to achieve the correct alignment. Multiple insertion/deletions are known to increase computation time from O(n2) to O(n3) although Gotoh has presented ...

Sequence alignment is an important task in bioinformatics which involves typical database search where data is in the form of DNA, RNA or protein sequence. For alignment various methods have been devised starting from pairwise alignment to multiple sequence alignment (MSA). To perform multiple sequence alignment various methods exists like progressive, iterative and concepts of dynamic programm...

We describe an new algorithm for visualizing an alignment of biological sequences according to a probabilistic model of evolution. The resulting data array is readily interpreted by the human eye and amenable to digital image techniques. We present examples using mRNA sequences from mouse and rat: three cytochromes and two zinc finger proteins. The underlying evolutionary model is derived from ...