Progressive multiple sequence alignments from triplets

Kruspe, Matthias; Stadler, Peter F.

doi:10.1186/1471-2105-8-254

Cited by 23 publications

(11 citation statements)

References 43 publications

(44 reference statements)

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“…. Alternatively, one might want to distinguish the probabilities that a base is paired upstream ( ξ < ), downstream ( ξ > ), or remains unpaired ( ξ 0 )

ξ_{i}^{<} = \sum_{j < i} P_{i j}, ξ_{i}^{>} = \sum_{j > i} P_{i j}, ξ^{0} = π_{i} - ξ_{i}^{>} - ξ_{i}^{<}

Distance measures derived from these three quantities have been used in particular in specialized structure‐aware sequence alignment algorithms for structured RNAs [Bonhoeffer et al, ; Dalli et al, ; Kruspe and Stadler, ].…”

Section: Methodsmentioning

confidence: 99%

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RNA snp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNP s

et al. 2013

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Structural characteristics are essential for the functioning of many noncoding RNAs and cis-regulatory elements of mRNAs. SNPs may disrupt these structures, interfere with their molecular function, and hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into structural effects of SNPs. The global measures employed so far suffer from limited accuracy of folding programs on large RNAs and are computationally too demanding for genome-wide applications. Here, we present a strategy that focuses on the local regions of maximal structural change between mutant and wild-type. These local regions are approximated in a “screening mode” that is intended for genome-wide applications. Furthermore, localized regions are identified as those with maximal discrepancy. The mutation effects are quantified in terms of empirical P values. To this end, the RNAsnp software uses extensive precomputed tables of the distribution of SNP effects as function of length and GC content. RNAsnp thus achieves both a noise reduction and speed-up of several orders of magnitude over shuffling-based approaches. On a data set comprising 501 SNPs associated with human-inherited diseases, we predict 54 to have significant local structural effect in the untranslated region of mRNAs. RNAsnp is available at http://rth.dk/resources/rnasnp.

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“…. Alternatively, one might want to distinguish the probabilities that a base is paired upstream ( ξ < ), downstream ( ξ > ), or remains unpaired ( ξ 0 )

ξ_{i}^{<} = \sum_{j < i} P_{i j}, ξ_{i}^{>} = \sum_{j > i} P_{i j}, ξ^{0} = π_{i} - ξ_{i}^{>} - ξ_{i}^{<}

Section: Methodsmentioning

confidence: 99%

“…Distance measures derived from these three quantities have been used in particular in specialized structure-aware sequence alignment algorithms for structured RNAs [Bonhoeffer et al, 1993;Dalli et al, 2006;Kruspe and Stadler, 2007].…”

Section: Structural (Dis)similaritiesmentioning

confidence: 99%

RNA snp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNP s

et al. 2013

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“…The same recursive structure easily generalizes to alignments of more than two sequences [8,38] even though the cost models need to be more restrictive to guarantee polynomial-time algorithms [31]. The computational effort for these exact solutions to the alignment problem increases exponentially with the number of sequences, hence only implementations for 3-way [20,32,34] and 4-way alignments [51] have gained practical importance. A wide variety of multiple sequence alignment problems (for arbitrary numbers of input sequences) have been shown to be NP-hard [6,14,28,30,56] and MAX SNP-hard [40,57].…”

Section: Introductionmentioning

confidence: 99%

“…The classical example is ClustalW [35]. The approach can be extended to starting from exact 3-way [32,34] or 4-way alignments [51].…”

Section: Introductionmentioning

confidence: 99%

Alignments as Compositional Structures

Berkemer¹,

Siederdissen²,

Stadler³

2018

Preprint

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Alignments, i.e., position-wise comparisons of two or more strings or ordered lists are of utmost practical importance in computational biology and a host of other fields, including historical linguistics and emerging areas of research in the Digital Humanities. The problem is well-known to be computationally hard as soon as the number of input strings is not bounded. Due to its practical importance, a huge number of heuristics have been devised, which have proved very successful in a wide range of applications. Alignments nevertheless have received hardly any attention as formal, mathematical structures. Here, we focus on the compositional aspects of alignments, which underlie most algorithmic approaches to computing alignments. We also show that the concepts naturally generalize to finite partially ordered sets and partial maps between them that in some sense preserve the partial orders.

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“…The computational problem of pinpointing the breakpoint position and identifying potentially duplicated or deleted sequence fragments can be understood as a specific mixture of local and global alignments of the three sequences F , R , and L , which we will formalize below. Three-way alignment algorithms have a long tradition in bioinformatics [ 21 , 22 ], where they have been used as components in progressive multiple sequence alignment procedures [ 23 , 24 ].…”

Section: Introductionmentioning

confidence: 99%

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements

Arab

Bernt

Tout

et al. 2017

Algorithms Mol Biol

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BackgroundGenomic DNA frequently undergoes rearrangement of the gene order that can be localized by comparing the two DNA sequences. In mitochondrial genomes different mechanisms are likely at work, at least some of which involve the duplication of sequence around the location of the apparent breakpoints. We hypothesize that these different mechanisms of genome rearrangement leave distinctive sequence footprints. In order to study such effects it is important to locate the breakpoint positions with precision.ResultsWe define a partially local sequence alignment problem that assumes that following a rearrangement of a sequence F, two fragments L, and R are produced that may exactly fit together to match F, leave a gap of deleted DNA between L and R, or overlap with each other. We show that this alignment problem can be solved by dynamic programming in cubic space and time. We apply the new method to evaluate rearrangements of animal mitogenomes and find that a surprisingly large fraction of these events involved local sequence duplications.ConclusionsThe partially local sequence alignment method is an effective way to investigate the mechanism of genomic rearrangement events. While applied here only to mitogenomes there is no reason why the method could not be used to also consider rearrangements in nuclear genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13015-017-0113-0) contains supplementary material, which is available to authorized users.

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Progressive multiple sequence alignments from triplets

Cited by 23 publications

References 43 publications

RNA snp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNP s

RNA snp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNP s

Alignments as Compositional Structures

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements

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