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On the Complexity of BWT-runs Minimization via Alphabet Reordering [article]

Jason Bentley, Daniel Gibney, Sharma V. Thankachan
2020 arXiv   pre-print
The Burrows-Wheeler Transform (BWT) has been an essential tool in text compression and indexing.  ...  Recently, there has been the development of compact suffix trees in space proportional to "r", the number of runs in the BWT, as well as the appearance of r in the time complexity of new algorithms.  ...  Since the alphabet size σ is linear in n, an 2 o(σ) time algorithm for AO would imply an 2 o(n) time algorithm for Hamiltonian Path.  ... 
arXiv:1911.03035v2 fatcat:s4d7ob36q5enxbe4hhaqzv7xfi

Prefix-Free Parsing for Building Big BWTs

Christina Boucher, Travis Gagie, Alan Kuhnle, Giovanni Manzini, Michael Wagner
2018 Workshop on Algorithms in Bioinformatics  
the BWT of T can be constructed from D and P using workspace proportional to their total size and O(|T |)-time.  ...  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  ...  In the final phase of the algorithm we compute the BWT of the input T .  ... 
doi:10.4230/lipics.wabi.2018.2 dblp:conf/wabi/BoucherGKM18 fatcat:6bghtxjmibhejjexjtnndcsr3u

Wheeler graphs: A framework for BWT-based data structures

Travis Gagie, Giovanni Manzini, Jouni Sirén
2017 Theoretical Computer Science  
We then rederive several variations of the BWT by designing straightforward finite-state automata for the relevant problems and showing that their state diagrams are Wheeler graphs.  ...  The famous Burrows-Wheeler Transform (BWT) was originally defined for a single string but variations have been developed for sets of strings, labeled trees, de Bruijn graphs, etc.  ...  Finally, we hope our new perspective on BWT variants makes them more accessible to computer scientists from areas outside string algorithms and data structures.  ... 
doi:10.1016/j.tcs.2017.06.016 pmid:29276331 pmcid:PMC5727778 fatcat:lon5o2wmwravdnyifdf3uvuate

LISA: Towards Learned DNA Sequence Search [article]

Darryl Ho, Jialin Ding, Sanchit Misra, Nesime Tatbul, Vikram Nathan, Vasimuddin Md, Tim Kraska
2019 arXiv   pre-print
LISA builds on and extends FM-index, which is the state-of-the-art technique widely deployed in genomics tool-chains.  ...  As a first proof of concept, we focus on accelerating one of the most essential flavors of the problem, called exact search.  ...  Acknowledgments We thank Tony Peng, Ashwath Thirumalai, and Elizabeth Wei for their contributions to the original design of LISA; and Pradeep Dubey and Heng Li for their valuable feedback.  ... 
arXiv:1910.04728v1 fatcat:jchmczupc5dfbevyikanfbbb6i

Bilateral Wilms Tumor: A Surgical Perspective

Andrew J Murphy, Andrew M Davidoff
2018 Children  
This review discusses the surgical management strategy in the context of BWT disease biology, with an emphasis on timepoints during therapy at which surgical decision making can greatly impact this disease  ...  Because of the risk of end-stage renal disease associated with the management of BWT, neoadjuvant chemotherapy and nephron-sparing surgery have been adopted as the guiding management principles.  ...  proliferative elements, or an alternate diagnosis (exceedingly uncommon).  ... 
doi:10.3390/children5100134 pmid:30250006 pmcid:PMC6210093 fatcat:mtmk7rkpfreunenhnejzob2k2e

Technology dictates algorithms: recent developments in read alignment

Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki (+5 others)
2021 Genome Biology  
AbstractAligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines.  ...  We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.  ...  Acknowledgements We thank the authors of the tools surveyed in this work for providing helpful feedback and verifying the information related to their tool.  ... 
doi:10.1186/s13059-021-02443-7 pmid:34446078 pmcid:PMC8390189 fatcat:wyk2y6ckpjempcpx45k5t34jnq

Parallel lossless data compression on the GPU

Ritesh A. Patel, Yao Zhang, Jason Mak, Andrew Davidson, John D. Owens
2012 2012 Innovative Parallel Computing (InPar)  
In particular, we utilize a two-level hierarchical sort for BWT, design a novel scan-based parallel MTF algorithm, and implement a parallel reduction scheme to build the Huffman tree.  ...  Our approach parallelizes three main stages in the bzip2 compression pipeline: Burrows-Wheeler transform (BWT), move-to-front transform (MTF), and Huffman coding.  ...  We appreciate the support of the HP Labs Innovation Research Program and the National Science Foundation (grants OCI-1032859 and CCF-1017399).  ... 
doi:10.1109/inpar.2012.6339599 fatcat:sjwuaayrwjbatgd6f7uttjt5la

Technology dictates algorithms: Recent developments in read alignment [article]

Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums (+4 others)
2020 arXiv   pre-print
Aligning reads onto reference genomes enables the identification of individual-specific genetic variants and is an essential step of the majority of genomic analysis pipelines.  ...  We provide rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read aligners.  ...  An alternative way to accelerate the alignment algorithms is by reducing the maximum number of differences that can be detected by the verification algorithm, which reduces the search space of the DP algorithm  ... 
arXiv:2003.00110v3 fatcat:3l3ad4z5xfhjxoo7snaskartxi

Evolution of biosequence search algorithms: a brief survey [article]

Gregory Kucherov
2018 arXiv   pre-print
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences.  ...  Finally, we focus on the transition to population genomics and outline associated algorithmic challenges.  ...  Seen from the computational perspective, the main question of population genomics is how to represent a collective genome of a population to allow an efficient algorithmic processing and, on the other  ... 
arXiv:1808.01038v4 fatcat:uiyjrwvgprgu3nfcu6i47o4wpe

FM-Index Reveals the Reverse Suffix Array

Arnab Ganguly, Daniel Gibney, Sahar Hooshmand, M. Oğuzhan Külekci, Sharma V. Thankachan, Oren Weimann, Inge Li Gørtz
2020 Annual Symposium on Combinatorial Pattern Matching  
Given a text T[1,n] over an alphabet Σ of size σ, the suffix array of T stores the lexicographic order of the suffixes of T.  ...  One can decode a suffix array value using the FM-Index in log^{O(1)} n time. We study an extension of the problem in which we have to also decode the suffix array values of the reverse text.  ...  The BWT of T is an array BWT[1, n] such that BWT[i] = T [SA[i] − 1], where T [0] = T [n].  ... 
doi:10.4230/lipics.cpm.2020.13 dblp:conf/cpm/0002GHKT20 fatcat:dcebr36dgvez7mlqyso7dsvljq

A New Burrows Wheeler Transform Markov Distance [article]

Edward Raff, Charles Nicholas, Mark McLean
2019 arXiv   pre-print
We describe issues with this approach that were not widely known, and introduce our new Burrows Wheeler Markov Distance (BWMD) as an alternative.  ...  Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems.  ...  The BWT takes an input string u of length n = |u|, over an alphabet Σ, and produces a new string u = bwt(u).  ... 
arXiv:1912.13046v1 fatcat:ijlx4t7v25ao3djlo43oimlcte

A New Burrows Wheeler Transform Markov Distance

Edward Raff, Charles Nicholas, Mark McLean
2020 PROCEEDINGS OF THE THIRTIETH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE AND THE TWENTY-EIGHTH INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE  
We describe issues with this approach that were not widely known, and introduce our new Burrows Wheeler Markov Distance (BWMD) as an alternative.  ...  Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems.  ...  The BWT takes an input string u of length n = |u|, over an alphabet Σ, and produces a new string u = bwt(u).  ... 
doi:10.1609/aaai.v34i04.5994 fatcat:5cm7gszwqfbkjdexfgqvgd55ea

Efficient in-memory top-k document retrieval

J. Shane Culpepper, Matthias Petri, Falk Scholer
2012 Proceedings of the 35th international ACM SIGIR conference on Research and development in information retrieval - SIGIR '12  
structures, and evaluate the various algorithmic trade-offs for performing efficient queries entirely in-memory.  ...  In this paper we present a hybrid algorithmic framework for inmemory bag-of-words ranked document retrieval using a self-index derived from the FM-Index, wavelet tree, and the compressed suffix tree data  ...  ACKNOWLEDGMENTS This work was supported in part by the Australian Research Council. We thank Gonzalo Navarro and Daniel Valenzuela for insightful discussions on the HSV method.  ... 
doi:10.1145/2348283.2348317 dblp:conf/sigir/CulpepperPS12 fatcat:izo2eeloyvgtdki6v7jev3zvmq

BowMapCL: Burrows-Wheeler Mapping on Multiple Heterogeneous Accelerators

David Nogueira, Pedro Tomas, Nuno Roma
2016 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
SOAP2; and up to 4Â faster than the best performing state-of-the-art GPU implementations (namely, SOAP3 and HPG-BWT).  ...  Contrasting to other alternatives, BowMapCL is based on a unified implementation using OpenCL, allowing the exploitation of multiple and possibly different devices (e.g., NVIDIA, AMD/ATI, and Intel GPUs  ...  To evaluate the performance of such alternative, it was devised an experiment to compare the two popcount implementations.  ... 
doi:10.1109/tcbb.2015.2495149 pmid:26529775 fatcat:d647a5w24rf7hbrqun7vbjtxta

Neural Representation of Natural Images in Visual Area V2

B. D. B. Willmore, R. J. Prenger, J. L. Gallant
2010 Journal of Neuroscience  
These results provide a new perspective on how complex shape selectivity arises, emphasizing the role of suppressive tuning in determining stimulus selectivity in higher visual cortex.  ...  Approximately one-half of the V2 neurons have tuning that is similar to V1. The other half of the V2 neurons are selective for complex features such as those that occur in natural scenes.  ...  The set of alternative models used was as follows. BWT plus center-surround.  ... 
doi:10.1523/jneurosci.4099-09.2010 pmid:20147538 pmcid:PMC2994536 fatcat:ndi7sautpbbf7gvoscecbgljyy
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