Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.

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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

We consider a problem of considerable practical interest: the recovery of a data matrix from a sampling of its entries. Suppose that we observe m entries selected uniformly at random from a matrix M. Can we complete the matrix and recover the entries that we have not seen?

We show that one can perfectly recover most low-rank matrices from what appears to be an incomplete set of entries. We prove that if the number m of sampled entries obeys $$m\ge C\,n^{1.2}r\log n$$ for some positive numerical constant C, then with very high probability, most n×n matrices of rank r can be perfectly recovered by solving a simple convex optimization program. This program finds the matrix with minimum nuclear norm that fits the data. The condition above assumes that the rank is not too large. However, if one replaces the 1.2 exponent with 1.25, then the result holds for all values of the rank. Similar results hold for arbitrary rectangular matrices as well. Our results are connected with the recent literature on compressed sensing, and show that objects other than signals and images can be perfectly reconstructed from very limited information.

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Exact Matrix Completion via Convex Optimization

We analyze the performance of a Genetic Type Algorithm we call Culling and a variety of other algorithms on a problem we refer to as ASP. Culling is near optimal for this problem, highly noise tolerant, and the best known a~~roach . . in some regimes. We show that the problem of learning the Ising perception is reducible to noisy ASP. These results provide an example of a rigorous analysis of GA’s and give insight into when and how C,A’s can beat competing methods. To analyze the genetic algorithm, we view it as a special type of submartingale. We prove some new large deviation bounds on this submartingale w~ich enable us to determine the running time of the algorithm.

On genetic algorithms

We present two algorithms for the approximate nearest neighbor problem in high-dimensional spaces. For data sets of size n living in R d , the algorithms require space that is only polynomial in n and d, while achieving query times that are sub-linear in n and polynomial in d. We also show applications to other high-dimensional geometric problems, such as the approximate minimum spanning tree. The article is based on the material from the authors' STOC'98 and FOCS'01 papers. It unifies, generalizes and simplifies the results from those papers.

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Approximate nearest neighbors: towards removing the curse of dimensionality

Covering the basic techniques used in the latest research work, the author consolidates progress made so far, including some very recent and promising results, and conveys the beauty and excitement of work in the field. He gives clear, lucid explanations of key results and ideas, with intuitive proofs, and provides critical examples and numerous illustrations to help elucidate the algorithms. Many of the results presented have been simplified and new insights provided. Of interest to theoretical computer scientists, operations researchers, and discrete mathematicians.

Approximation Algorithms

We present several approximation algorithms for the problem of embedding metric spaces into a line, and into the 2-dimensional plane. Among other results, we give an $O(\sqrt{n})$-approximation alg...

Approximation Algorithms for Low-Distortion Embeddings into Low-Dimensional Spaces

The paper promotes the study of computational aspects, primarily the convergence rate, of nonlinear dynamical systems from a combinatorial perspective. The authors identify the class of symmetric quadratic systems. Such systems have been widely used to model phenomena in the natural sciences, and also provide an appropriate framework for the study of genetic algorithms in combinatorial optimisation. They prove several fundamental general properties of these systems, notably that every trajectory converges to a fixed point. They go on to give a detailed analysis of a quadratic system defined in a natural way on probability distributions over the set of matchings in a graph. In particular, they prove that convergence to the limit requires only polynomial time when the graph is a tree. This result demonstrates that such systems, though nonlinear, are amenable to quantitative analysis. >

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Quadratic dynamical systems

We present several approximation algorithms for the problem of embedding metric spaces into a line, and into the two-dimensional plane. Among other results, we give an O(√n)-approximation algorithm for the problem of finding a line embedding of a metric induced by a given unweighted graph, that minimizes the (standard) multiplicative distortion. We give an improved O(n1/3) approximation for the case of metrics generated by unweighted trees. This is the first result of this type.

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Approximation algorithms for low-distortion embeddings into low-dimensional spaces

We show that the shortest-path metric of any $k$-outerplanar graph, for any fixed $k$, can be approximated by a probability distribution over tree metrics with constant distortion and hence also embedded into $\ell_1$ with constant distortion. These graphs play a central role in polynomial time approximation schemes for many NP-hard optimization problems on general planar graphs and include the family of weighted $k\times n$ planar grids. This result implies a constant upper bound on the ratio between the sparsest cut and the maximum concurrent flow in multicommodity networks for $k$-outerplanar graphs, thus extending a theorem of Okamura and Seymour [J. Combin. Theory Ser. B, 31 (1981), pp. 75-81] for outerplanar graphs, and a result of Gupta et al. [Combinatorica, 24 (2004), pp. 233-269] for treewidth-2 graphs. In addition, we obtain improved approximation ratios for $k$-outerplanar graphs on various problems for which approximation algorithms are based on probabilistic tree embeddings. We conjecture that these embeddings for $k$-outerplanar graphs may serve as building blocks for $\ell_1$ embeddings of more general metrics.

Yuri Rabinovich

Papers

Approximation Algorithms for Low-Distortion Embeddings into Low-Dimensional Spaces

Quadratic dynamical systems

Approximation algorithms for low-distortion embeddings into low-dimensional spaces

Embedding k -Outerplanar Graphs into l 1

A computational view of population genetics