Results 241 to 250 of about 67,014 (277)
Some of the next articles are maybe not open access.
2014
Intuitively, if two strings S 1 and S 2 are sufficiently similar and we already have an FM-index for S 1 then, by storing a little extra information, we should be able to reuse parts of that index in an FM-index for S 2. We formalize this intuition and show that it can lead to significant space savings in practice, as well as to some interesting ...
Belazzougui Djamal +4 more
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Intuitively, if two strings S 1 and S 2 are sufficiently similar and we already have an FM-index for S 1 then, by storing a little extra information, we should be able to reuse parts of that index in an FM-index for S 2. We formalize this intuition and show that it can lead to significant space savings in practice, as well as to some interesting ...
Belazzougui Djamal +4 more
openaire +2 more sources
2004
We show that, by combining an existing compression boosting technique with the wavelet tree data structure, we are able to design a variant of the FM-index which scales well with the size of the input alphabet Σ. The size of the new index built on a string T[1,n] is bounded by \(n H_{k}(T) + O\bigl((n \log\log n)/\log_{\vert {\Sigma}\vert } n\bigr ...
FERRAGINA, PAOLO +3 more
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We show that, by combining an existing compression boosting technique with the wavelet tree data structure, we are able to design a variant of the FM-index which scales well with the size of the input alphabet Σ. The size of the new index built on a string T[1,n] is bounded by \(n H_{k}(T) + O\bigl((n \log\log n)/\log_{\vert {\Sigma}\vert } n\bigr ...
FERRAGINA, PAOLO +3 more
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Compressing Similar Biological Sequences Using FM-Index
2014 Data Compression Conference, 2014Nowadays, decreasing cost and better accessibility of sequencing methods have enabled studies of genetic variation between individuals of the same species and also between two related species. This has led to a rapid increase in biological data consisting of sequences that are very similar to each other, these sequences usually being stored together in
Petr Prochazka, Jan Holub
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String Matching in Hardware Using the FM-Index
2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, 2011String matching is a ubiquitous problem that arises in a wide range of applications in computing, e.g., packet routing, intrusion detection, web querying, and genome analysis. Due to its importance, dozens of algorithms and several data structures have been developed over the years.
Edward Fernandez +2 more
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Accelerating FM-index Search for Genomic Data Processing
Proceedings of the 47th International Conference on Parallel Processing, 2018The deluge of genomics data is incurring prohibitively high computational costs. As an important building block for genomic data processing algorithms, FM-index search occupies most of execution time in sequence alignment. Due to massive random streaming memory references relative to only small amount of computations, FM-index search algorithm exhibits
Yuanrong Wang +4 more
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Hybrid Compression of Bitvectors for the FM-Index
2014 Data Compression Conference, 2014Compressed bit vectors supporting rank and select operations are the workhorse of compressed data structures. We propose a hybrid scheme for implementing compressed bit vectors, which divides the bit vector into blocks and then chooses the encoding of each block separately from a number of different encoding methods.
Kempa Dominik +2 more
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Short read error correction using an FM-index
2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015Whole genome sequencing is becoming more affordable, but sequencing errors complicate the analysis and diminish the utility of the data. We present FMRC, a new tool for correcting errors in DNA short reads from high-throughput sequencing. It uses a Burrows-Wheeler Transform and FM-index to enable a k-mer counting approach for correcting substitution ...
Seth Greenstein +2 more
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Complementary Contextual Models with FM-Index for DNA Compression
2017 Data Compression Conference (DCC), 2017Demanding for efficient compression and storage of DNA sequences has been rising with the rapid growth of DNA sequencing technologies. Existing reference-based algorithms map all patterns to regions found in the reference sequence, which lead to redundancy of incomplete similarity.
Wenjing Fan +3 more
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Effect of Intensity Modulation on Measuring of FM Index
Journal of Optical Communications, 2000This paper derives an exact expression to compute the magnitude of the optical line spectrum when DFB laser is directly modulated by sinusoidal signal. Measuring technique using scanning Fabry-Perot interferometer (FPI) to compute the frequency modulation (FM) index of the laser diode (LD) have been reported in earlier literature.
Chew, Y.H., Tjhung, T.T.
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Design of Overlapping Block FM-Index Based on Distributed Environment
2009 International Forum on Information Technology and Applications, 2009With the development of networks and database, the rapid growth of information and data, data files pose a challenge to information retrieval. Compression technology archived the query in the compressed state. Compression enquiries index FM-index is an advanced algorithm in the field, but FM-index must consume great memory in process of construct index.
Jun Liang +4 more
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