461 research outputs found
Simulating the DNA Overlap Graph in Succinct Space
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph (dBG) of some order k. Each has advantages over the other depending on the application. Still, the ideal setting would be to have an index of the reads that is easy to build and can be adapted to any type of biological analysis. In this paper we propose rBOSS, a new data structure based on the Burrows-Wheeler Transform (BWT), which gets close to that ideal. Our rBOSS simultaneously encodes all the dBGs of a set of sequencing reads up to some order k, and for any dBG node v, it can compute in O(k) time all the other nodes whose labels have an overlap of at least m characters with the label of v, with m being a parameter. If we choose the parameter k equal to the size of the reads (assuming that all have equal length), then we can simulate the overlap graph of the read set. Instead of storing the edges of this graph explicitly, rBOSS computes them on the fly as we traverse the graph. As most BWT-based structures, rBOSS is unidirectional, meaning that we can retrieve only the suffix overlaps of the nodes. However, we exploit the property of the DNA reverse complements to simulate bi-directionality. We implemented a genome assembler on top of rBOSS to demonstrate its usefulness. The experimental results show that, using k=100, our rBOSS-based assembler can process ~500K reads of 150 characters long each (a FASTQ file of 185 MB) in less than 15 minutes and using 110 MB in total. It produces contigs of mean sizes over 10,000, which is twice the size obtained by using a pure de Bruijn graph of fixed length k
Improved ESP-index: a practical self-index for highly repetitive texts
While several self-indexes for highly repetitive texts exist, developing a
practical self-index applicable to real world repetitive texts remains a
challenge. ESP-index is a grammar-based self-index on the notion of
edit-sensitive parsing (ESP), an efficient parsing algorithm that guarantees
upper bounds of parsing discrepancies between different appearances of the same
subtexts in a text. Although ESP-index performs efficient top-down searches of
query texts, it has a serious issue on binary searches for finding appearances
of variables for a query text, which resulted in slowing down the query
searches. We present an improved ESP-index (ESP-index-I) by leveraging the idea
behind succinct data structures for large alphabets. While ESP-index-I keeps
the same types of efficiencies as ESP-index about the top-down searches, it
avoid the binary searches using fast rank/select operations. We experimentally
test ESP-index-I on the ability to search query texts and extract subtexts from
real world repetitive texts on a large-scale, and we show that ESP-index-I
performs better that other possible approaches.Comment: This is the full version of a proceeding accepted to the 11th
International Symposium on Experimental Algorithms (SEA2014
Prospects and limitations of full-text index structures in genome analysis
The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared
Space-time Trade-offs for the LCP Array of Wheeler DFAs
Recently, Conte et al. generalized the longest-common prefix (LCP) array from
strings to Wheeler DFAs, and they showed that it can be used to efficiently
determine matching statistics on a Wheeler DFA [DCC 2023]. However, storing the
LCP array requires bits, being the number of states,
while the compact representation of Wheeler DFAs often requires much less
space. In particular, the BOSS representation of a de Bruijn graph only
requires a linear number of bits, if the size of alphabet is constant.
In this paper, we propose a sampling technique that allows to access an entry
of the LCP array in logarithmic time by only storing a linear number of bits.
We use our technique to provide a space-time trade-off to compute matching
statistics on a Wheeler DFA. In addition, we show that by augmenting the BOSS
representation of a -th order de Bruijn graph with a linear number of bits
we can navigate the underlying variable-order de Bruijn graph in time
logarithmic in , thus improving a previous bound by Boucher et al. which
was linear in [DCC 2015]
Better Safe Than Sorry: An Adversarial Approach to Improve Social Bot Detection
The arm race between spambots and spambot-detectors is made of several cycles
(or generations): a new wave of spambots is created (and new spam is spread),
new spambot filters are derived and old spambots mutate (or evolve) to new
species. Recently, with the diffusion of the adversarial learning approach, a
new practice is emerging: to manipulate on purpose target samples in order to
make stronger detection models. Here, we manipulate generations of Twitter
social bots, to obtain - and study - their possible future evolutions, with the
aim of eventually deriving more effective detection techniques. In detail, we
propose and experiment with a novel genetic algorithm for the synthesis of
online accounts. The algorithm allows to create synthetic evolved versions of
current state-of-the-art social bots. Results demonstrate that synthetic bots
really escape current detection techniques. However, they give all the needed
elements to improve such techniques, making possible a proactive approach for
the design of social bot detection systems.Comment: This is the pre-final version of a paper accepted @ 11th ACM
Conference on Web Science, June 30-July 3, 2019, Boston, U
Relative Suffix Trees
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.Peer reviewe
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