40 Search Results for "Parida, Laxmi"


Volume

LIPIcs, Volume 113

18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

WABI 2018, August 20-22, 2018, Helsinki, Finland

Editors: Laxmi Parida and Esko Ukkonen

Document
Complete Volume
LIPIcs, Volume 113, WABI'18, Complete Volume

Authors: Laxmi Parida and Esko Ukkonen

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
LIPIcs, Volume 113, WABI'18, Complete Volume

Cite as

Laxmi Parida and Esko Ukkonen. LIPIcs, Volume 113, WABI'18, Complete Volume. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@Proceedings{parida_et_al:LIPIcs.WABI.2018,
  title =	{{LIPIcs, Volume 113, WABI'18, Complete Volume}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018},
  URN =		{urn:nbn:de:0030-drops-97246},
  doi =		{10.4230/LIPIcs.WABI.2018},
  annote =	{Keywords: Applied computing, Bioinformatics, Theory of computation, Design and analysis of algorithms, Mathematics of computing, Probabilistic inference problem}
}
Document
Front Matter
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Laxmi Parida and Esko Ukkonen

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
Front Matter, Table of Contents, Preface, Conference Organization

Cite as

Laxmi Parida and Esko Ukkonen. Front Matter, Table of Contents, Preface, Conference Organization. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 0:i-0:xvi, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{parida_et_al:LIPIcs.WABI.2018.0,
  author =	{Parida, Laxmi and Ukkonen, Esko},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{0:i--0:xvi},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.0},
  URN =		{urn:nbn:de:0030-drops-93028},
  doi =		{10.4230/LIPIcs.WABI.2018.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models

Authors: Hooman Zabeti, Tamon Stephen, Bonnie Berger, and Leonid Chindelevitch

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
Elemental balance, the property of having the same number of each type of atom on both sides of the equation, is a fundamental feature of chemical reactions. In metabolic network models, this property is typically verified on a reaction-by-reaction basis. In this paper we show how violations of elemental balance can be efficiently detected in an entire network, without the need for specifying the chemical formula of each of the metabolites, which enhances a modeler's ability to automatically verify that their model satisfies elemental balance. Our method makes use of duality theory, linear programming, and mixed integer linear programming, and runs efficiently on genome-scale metabolic networks (GSMNs). We detect elemental balance violations in 40 out of 84 metabolic network models in the BiGG database. We also identify a short list of reactions that are candidates for being elementally imbalanced. Out of these candidates, nearly half turn out to be truly imbalanced reactions, and the rest can be seen as witnesses of elemental balance violations elsewhere in the network. The majority of these violations involve a proton imbalance, a known challenge of metabolic network reconstruction. Our approach is efficient, easy to use and powerful. It can be helpful to metabolic network modelers during model verification. Our methods are fully integrated into the MONGOOSE software suite and are available at https://github.com/WGS-TB/MongooseGUI3.

Cite as

Hooman Zabeti, Tamon Stephen, Bonnie Berger, and Leonid Chindelevitch. A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 1:1-1:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{zabeti_et_al:LIPIcs.WABI.2018.1,
  author =	{Zabeti, Hooman and Stephen, Tamon and Berger, Bonnie and Chindelevitch, Leonid},
  title =	{{A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{1:1--1:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.1},
  URN =		{urn:nbn:de:0030-drops-93034},
  doi =		{10.4230/LIPIcs.WABI.2018.1},
  annote =	{Keywords: Metabolic network analysis, elemental imbalance, linear programming, model verification}
}
Document
Prefix-Free Parsing for Building Big BWTs

Authors: Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such indexes is a challenge. Fortunately, many of these genomic databases are highly-repetitive - a characteristic that can be exploited and enable the computation of the Burrows-Wheeler Transform (BWT), which underlies many popular indexes. In this paper, we introduce a preprocessing algorithm, referred to as prefix-free parsing, that takes a text T as input, and in one-pass generates a dictionary D and a parse P of T with the property that the BWT of T can be constructed from D and P using workspace proportional to their total size and O(|T|)-time. Our experiments show that D and P are significantly smaller than T in practice, and thus, can fit in a reasonable internal memory even when T is very large. Therefore, prefix-free parsing eases BWT construction, which is pertinent to many bioinformatics applications.

Cite as

Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini. Prefix-Free Parsing for Building Big BWTs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 2:1-2:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{boucher_et_al:LIPIcs.WABI.2018.2,
  author =	{Boucher, Christina and Gagie, Travis and Kuhnle, Alan and Manzini, Giovanni},
  title =	{{Prefix-Free Parsing for Building Big BWTs}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{2:1--2:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.2},
  URN =		{urn:nbn:de:0030-drops-93044},
  doi =		{10.4230/LIPIcs.WABI.2018.2},
  annote =	{Keywords: Burrows-Wheeler Transform, prefix-free parsing, compression-aware algorithms, genomic databases}
}
Document
Detecting Mutations by eBWT

Authors: Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts how many copies of any nucleotide are expected inside each such cluster, and how an elegant and precise LCP array based procedure can locate these clusters in the eBWT. Our findings are very general and can be applied to a wide range of different problems. In this paper, we consider the case of alignment-free and reference-free SNPs discovery in multiple collections of reads. We note that, in accordance with our theoretical results, SNPs are clustered in the eBWT of the reads collection, and we develop a tool finding SNPs with a simple scan of the eBWT and LCP arrays. Preliminary results show that our method requires much less coverage than state-of-the-art tools while drastically improving precision and sensitivity.

Cite as

Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone. Detecting Mutations by eBWT. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 3:1-3:15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{prezza_et_al:LIPIcs.WABI.2018.3,
  author =	{Prezza, Nicola and Pisanti, Nadia and Sciortino, Marinella and Rosone, Giovanna},
  title =	{{Detecting Mutations by eBWT}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{3:1--3:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.3},
  URN =		{urn:nbn:de:0030-drops-93051},
  doi =		{10.4230/LIPIcs.WABI.2018.3},
  annote =	{Keywords: BWT, LCP Array, SNPs, Reference-free, Assembly-free}
}
Document
Haplotype-aware graph indexes

Authors: Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict J. Paten, and Richard Durbin

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information to identify which paths are more likely to be correct. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by indexing the 1000 Genomes Project haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.

Cite as

Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict J. Paten, and Richard Durbin. Haplotype-aware graph indexes. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 4:1-4:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{siren_et_al:LIPIcs.WABI.2018.4,
  author =	{Sir\'{e}n, Jouni and Garrison, Erik and Novak, Adam M. and Paten, Benedict J. and Durbin, Richard},
  title =	{{Haplotype-aware graph indexes}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{4:1--4:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.4},
  URN =		{urn:nbn:de:0030-drops-93060},
  doi =		{10.4230/LIPIcs.WABI.2018.4},
  annote =	{Keywords: FM-indexes, variation graphs, haplotypes}
}
Document
Reconciling Multiple Genes Trees via Segmental Duplications and Losses

Authors: Riccardo Dondi, Manuel Lafond, and Celine Scornavacca

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost delta and lambda, respectively. We show that the problem is polynomial-time solvable when delta <= lambda (via LCA-mapping), while if delta > lambda the problem is NP-hard, even when lambda = 0 and a single gene tree is given, solving a long standing open problem on the complexity of the reconciliation problem. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are delta/lambda and the number d of segmental duplications, of time complexity O(ceil[delta/lambda]^d * n * delta/lambda). Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or refute hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.

Cite as

Riccardo Dondi, Manuel Lafond, and Celine Scornavacca. Reconciling Multiple Genes Trees via Segmental Duplications and Losses. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 5:1-5:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{dondi_et_al:LIPIcs.WABI.2018.5,
  author =	{Dondi, Riccardo and Lafond, Manuel and Scornavacca, Celine},
  title =	{{Reconciling Multiple Genes Trees via Segmental Duplications and Losses}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{5:1--5:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.5},
  URN =		{urn:nbn:de:0030-drops-93079},
  doi =		{10.4230/LIPIcs.WABI.2018.5},
  annote =	{Keywords: Gene trees/species tree reconciliation, phylogenetics, computational complexity, fixed-parameter algorithms}
}
Document
Protein Classification with Improved Topological Data Analysis

Authors: Tamal K. Dey and Sayan Mandal

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
Automated annotation and analysis of protein molecules have long been a topic of interest due to immediate applications in medicine and drug design. In this work, we propose a topology based, fast, scalable, and parameter-free technique to generate protein signatures. We build an initial simplicial complex using information about the protein's constituent atoms, including its radius and existing chemical bonds, to model the hierarchical structure of the molecule. Simplicial collapse is used to construct a filtration which we use to compute persistent homology. This information constitutes our signature for the protein. In addition, we demonstrate that this technique scales well to large proteins. Our method shows sizable time and memory improvements compared to other topology based approaches. We use the signature to train a protein domain classifier. Finally, we compare this classifier against models built from state-of-the-art structure-based protein signatures on standard datasets to achieve a substantial improvement in accuracy.

Cite as

Tamal K. Dey and Sayan Mandal. Protein Classification with Improved Topological Data Analysis. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 6:1-6:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{dey_et_al:LIPIcs.WABI.2018.6,
  author =	{Dey, Tamal K. and Mandal, Sayan},
  title =	{{Protein Classification with Improved Topological Data Analysis}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{6:1--6:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.6},
  URN =		{urn:nbn:de:0030-drops-93082},
  doi =		{10.4230/LIPIcs.WABI.2018.6},
  annote =	{Keywords: topological data analysis, persistent homology, simplicial collapse, supervised learning, topology based protein feature vector, protein classification}
}
Document
A Dynamic Algorithm for Network Propagation

Authors: Barak Sternberg and Roded Sharan

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
Network propagation is a powerful transformation that amplifies signal-to-noise ratio in biological and other data. To date, most of its applications in the biological domain employed standard techniques for its computation that require O(m) time for a network with n vertices and m edges. When applied in a dynamic setting where the network is constantly modified, the cost of these computations becomes prohibitive. Here we study, for the first time in the biological context, the complexity of dynamic algorithms for network propagation. We develop a vertex decremental algorithm that is motivated by various biological applications and can maintain propagation scores over general weights at an amortized cost of O(m/(n^{1/4})) per update. In application to real networks, the dynamic algorithm achieves significant, 50- to 100-fold, speedups over conventional static methods for network propagation, demonstrating its great potential in practice.

Cite as

Barak Sternberg and Roded Sharan. A Dynamic Algorithm for Network Propagation. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 7:1-7:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{sternberg_et_al:LIPIcs.WABI.2018.7,
  author =	{Sternberg, Barak and Sharan, Roded},
  title =	{{A Dynamic Algorithm for Network Propagation}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{7:1--7:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.7},
  URN =		{urn:nbn:de:0030-drops-93095},
  doi =		{10.4230/LIPIcs.WABI.2018.7},
  annote =	{Keywords: Network propagation, Dynamic graph algorithm, protein-protein interaction network}
}
Document
New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy

Authors: Qiuyi (Richard) Zhang, Satish Rao, and Tandy Warnow

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
Absolute fast converging (AFC) phylogeny estimation methods are ones that have been proven to recover the true tree with high probability given sequences whose lengths are polynomial in the number of number of leaves in the tree (once the shortest and longest branch lengths are fixed). While there has been a large literature on AFC methods, the best in terms of empirical performance was DCM_NJ, published in SODA 2001. The main empirical advantage of DCM_NJ over other AFC methods is its use of neighbor joining (NJ) to construct trees on smaller taxon subsets, which are then combined into a tree on the full set of species using a supertree method; in contrast, the other AFC methods in essence depend on quartet trees that are computed independently of each other, which reduces accuracy compared to neighbor joining. However, DCM_NJ is unlikely to scale to large datasets due to its reliance on supertree methods, as no current supertree methods are able to scale to large datasets with high accuracy. In this study we present a new approach to large-scale phylogeny estimation that shares some of the features of DCM_NJ but bypasses the use of supertree methods. We prove that this new approach is AFC and uses polynomial time. Furthermore, we describe variations on this basic approach that can be used with leaf-disjoint constraint trees (computed using methods such as maximum likelihood) to produce other AFC methods that are likely to provide even better accuracy. Thus, we present a new generalizable technique for large-scale tree estimation that is designed to improve scalability for phylogeny estimation methods to ultra-large datasets, and that can be used in a variety of settings (including tree estimation from unaligned sequences, and species tree estimation from gene trees).

Cite as

Qiuyi (Richard) Zhang, Satish Rao, and Tandy Warnow. New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 8:1-8:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{zhang_et_al:LIPIcs.WABI.2018.8,
  author =	{Zhang, Qiuyi (Richard) and Rao, Satish and Warnow, Tandy},
  title =	{{New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{8:1--8:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.8},
  URN =		{urn:nbn:de:0030-drops-93108},
  doi =		{10.4230/LIPIcs.WABI.2018.8},
  annote =	{Keywords: phylogeny estimation, short quartets, sample complexity, absolute fast converging methods, neighbor joining, maximum likelihood}
}
Document
An Average-Case Sublinear Exact Li and Stephens Forward Algorithm

Authors: Yohei M. Rosen and Benedict J. Paten

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
Hidden Markov models of haplotype inheritance such as the Li and Stephens model allow for computationally tractable probability calculations using the forward algorithms as long as the representative reference panel used in the model is sufficiently small. Specifically, the monoploid Li and Stephens model and its variants are linear in reference panel size unless heuristic approximations are used. However, sequencing projects numbering in the thousands to hundreds of thousands of individuals are underway, and others numbering in the millions are anticipated. To make the Li and Stephens forward algorithm for these datasets computationally tractable, we have created a numerically exact version of the algorithm with observed average case O(nk^{0.35}) runtime in number of genetic sites n and reference panel size k. This avoids any tradeoff between runtime and model complexity. We demonstrate that our approach also provides a succinct data structure for general purpose haplotype data storage. We discuss generalizations of our algorithmic techniques to other hidden Markov models.

Cite as

Yohei M. Rosen and Benedict J. Paten. An Average-Case Sublinear Exact Li and Stephens Forward Algorithm. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 9:1-9:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{rosen_et_al:LIPIcs.WABI.2018.9,
  author =	{Rosen, Yohei M. and Paten, Benedict J.},
  title =	{{An Average-Case Sublinear Exact Li and Stephens Forward Algorithm}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{9:1--9:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.9},
  URN =		{urn:nbn:de:0030-drops-93116},
  doi =		{10.4230/LIPIcs.WABI.2018.9},
  annote =	{Keywords: Haplotype, Hidden Markov Model, Forward Algorithm, Lazy Evaluation}
}
Document
External memory BWT and LCP computation for sequence collections with applications

Authors: Lavinia Egidi, Felipe A. Louza, Giovanni Manzini, and Guilherme P. Telles

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input parameter, and tries to make the best use of it by splitting the input collection into subcollections sufficiently small that it can compute their BWT in RAM using an optimal linear time algorithm. Next, it merges the partial BWTs in external memory and in the process it also computes the LCP values. We show that our algorithm performs O(n maxlcp) sequential I/Os, where n is the total length of the collection and maxlcp is the maximum LCP value. The experimental results show that our algorithm outperforms the current best algorithm for collections of sequences with different lengths and when the average LCP of the collection is relatively small compared to the length of the sequences. In the second part of the paper, we show that our algorithm can be modified to output two additional arrays that, combined with the BWT and LCP arrays, provide simple, scan based, external memory algorithms for three well known problems in bioinformatics: the computation of the all pairs suffix-prefix overlaps, the computation of maximal repeats, and the construction of succinct de Bruijn graphs.

Cite as

Lavinia Egidi, Felipe A. Louza, Giovanni Manzini, and Guilherme P. Telles. External memory BWT and LCP computation for sequence collections with applications. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 10:1-10:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


Copy BibTex To Clipboard

@InProceedings{egidi_et_al:LIPIcs.WABI.2018.10,
  author =	{Egidi, Lavinia and Louza, Felipe A. and Manzini, Giovanni and Telles, Guilherme P.},
  title =	{{External memory BWT and LCP computation for sequence collections with applications}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{10:1--10:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.10},
  URN =		{urn:nbn:de:0030-drops-93122},
  doi =		{10.4230/LIPIcs.WABI.2018.10},
  annote =	{Keywords: Burrows-Wheeler Transform, Longest Common Prefix Array, All pairs suffix-prefix overlaps, Succinct de Bruijn graph, Maximal repeats}
}
Document
Kermit: Guided Long Read Assembly using Coloured Overlap Graphs

Authors: Riku Walve, Pasi Rastas, and Leena Salmela

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assembly of long reads is still challenging and often results in a large collection of contigs. Dense linkage maps are collections of markers whose location on the genome is approximately known. Therefore they provide long range information that has the potential to greatly aid in de novo assembly. Previously linkage maps have been used to detect misassemblies and to manually order contigs. However, no fully automated tools exist to incorporate linkage maps in assembly but instead large amounts of manual labour is needed to order the contigs into chromosomes. We formulate the genome assembly problem in the presence of linkage maps and present the first method for guided genome assembly using linkage maps. Our method is based on an additional cleaning step added to the assembly. We show that it can simplify the underlying assembly graph, resulting in more contiguous assemblies and reducing the amount of misassemblies when compared to de novo assembly.

Cite as

Riku Walve, Pasi Rastas, and Leena Salmela. Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 11:1-11:11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


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@InProceedings{walve_et_al:LIPIcs.WABI.2018.11,
  author =	{Walve, Riku and Rastas, Pasi and Salmela, Leena},
  title =	{{Kermit: Guided Long Read Assembly using Coloured Overlap Graphs}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{11:1--11:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.11},
  URN =		{urn:nbn:de:0030-drops-93135},
  doi =		{10.4230/LIPIcs.WABI.2018.11},
  annote =	{Keywords: Genome assembly, Linkage maps, Coloured overlap graph}
}
Document
A Succinct Solution to Rmap Alignment

Authors: Martin D. Muggli, Simon J. Puglisi, and Christina Boucher

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


Abstract
We present Kohdista, which is an index-based algorithm for finding pairwise alignments between single molecule maps (Rmaps). The novelty of our approach is the formulation of the alignment problem as automaton path matching, and the application of modern index-based data structures. In particular, we combine the use of the Generalized Compressed Suffix Array (GCSA) index with the wavelet tree in order to build Kohdista. We validate Kohdista on simulated E. coli data, showing the approach successfully finds alignments between Rmaps simulated from overlapping genomic regions. Lastly, we demonstrate Kohdista is the only method that is capable of finding a significant number of high quality pairwise Rmap alignments for large eukaryote organisms in reasonable time. Kohdista is available at https://github.com/mmuggli/KOHDISTA/.

Cite as

Martin D. Muggli, Simon J. Puglisi, and Christina Boucher. A Succinct Solution to Rmap Alignment. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 12:1-12:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)


Copy BibTex To Clipboard

@InProceedings{muggli_et_al:LIPIcs.WABI.2018.12,
  author =	{Muggli, Martin D. and Puglisi, Simon J. and Boucher, Christina},
  title =	{{A Succinct Solution to Rmap Alignment}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.12},
  URN =		{urn:nbn:de:0030-drops-93143},
  doi =		{10.4230/LIPIcs.WABI.2018.12},
  annote =	{Keywords: Optical mapping, index based data structures, FM-index, graph algorithms}
}
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