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Constructing Aligned Sequence Blocks
Journal of Computational Biology, 1994This paper presents an efficient method for constructing aligned blocks (i.e., gap-free multiple alignments) from a set of pairwise alignments. The method is more sensitive than some earlier block-constructing methods for detecting conserved sequence regions.
W, Miller +4 more
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Multiple protein sequence alignment
Current Opinion in Structural Biology, 2008Multiple sequence alignments are essential in computational analysis of protein sequences and structures, with applications in structure modeling, functional site prediction, phylogenetic analysis and sequence database searching. Constructing accurate multiple alignments for divergent protein sequences remains a difficult computational task, and ...
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Near-optimal sequence alignment
Current Opinion in Structural Biology, 1996Recent advances in algorithmic techniques and statistics of sequence alignment have helped to make near-optimal alignments an important tool in the delineation of biologically valid alignments. Near-optimal alignments serve to judge the reliability of portions of a sequence alignment.
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Ggmsa: a Visual Exploration Tool for Multiple Sequence Alignment and Associated Data
Briefings Bioinform., 2022Lang Zhou +12 more
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Aligning Sequences to Structures
2007Most newly sequenced proteins are likely to adopt a similar structure to one which has already been experimentally determined. For this reason, the most successful approaches to protein structure prediction have been template-based methods. Such prediction methods attempt to identify and model the folds of unknown structures by aligning the target ...
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Efficient sequence alignment algorithms
Journal of Theoretical Biology, 1984Sequence 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(
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DNA multiple sequence alignments
2002In this chapter we examine the procedure of multiple sequence alignment. We first examine the heuristic procedures commonly used in multiple sequence alignment. Next we examine sources of ambiguity involved in the alignment procedure. We suggest that several alignment parameters be employed to examine alignment sensitivity.
Gonzalo, Giribet +2 more
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Bioinformatics, 1994
We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time.
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We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time.
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Cancer epigenetics in clinical practice
Ca-A Cancer Journal for Clinicians, 2023Veronica Davalos, Manel Esteller
exaly