Results 131 to 140 of about 4,611,263 (171)

Hybrid Compression of Bitvectors for the FM-Index

2014 Data Compression Conference, 2014
Compressed 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.
Juha Kärkkäinen, Dominik Kempa, S. Puglisi   +2 more
semanticscholar   +2 more sources

Accelerating FM-index Search for Genomic Data Processing

Proceedings of the 47th International Conference on Parallel Processing, 2018
The 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
Yuanrong Wang, Xueqi Li, Dawei Zang, Guangming Tan, Ninghui Sun   +4 more
semanticscholar   +2 more sources

Complementary Contextual Models with FM-Index for DNA Compression

2017 Data Compression Conference (DCC), 2017
Demanding 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, Wenrui Dai, Yong Li, H. Xiong   +3 more
semanticscholar   +2 more sources

String Matching in Hardware Using the FM-Index

2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, 2011
String 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, W. Najjar, Stefano Lonardi   +2 more
semanticscholar   +2 more sources

Optimizing the Performance of the FM-Index for Large-Scale Data

The Expanding World of Compressed Data
The FM-index is a fundamental data structure used in bioinformatics to efficiently search for strings and index genomes. However, the FM-index can pose computational challenges, particularly in the context of large-scale genomic datasets, due to the complexity of its underlying components and data encodings.
Eddie Ferro, C. Boucher
semanticscholar   +3 more sources

Short read error correction using an FM-index

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015
Whole 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, J. Holt, L. McMillan
semanticscholar   +2 more sources

FM-Adaptive: A Practical Data-Aware FM-Index

The Expanding World of Compressed Data
The FM-index provides an important solution for efficient retrieval and search in textual big data. Its variants have been widely used in many fields including information retrieval, genome analysis, and web searching. In this paper, we propose improvements via a new compressed representation of the wavelet tree of the Burrows-Wheeler transform of the ...
Hongwei Huo, Zongtao He, Pengfei Liu, Jeffrey Scott Vitter   +3 more
semanticscholar   +3 more sources

An FM-Index Based High-Throughput Memory-Efficient FPGA Accelerator for Paired-End Short-Read Mapping

IEEE Transactions on Biomedical Circuits and Systems, 2023
This article presents an Ferragina-Manzini index (FM-index) based paired-end short-read mapping hardware accelerator. Four techniques are proposed to significantly reduce the number of memory accesses and operations to improve the throughput.
Chung-Hsuan Yang, Yi-Chung Wu, Yen-Lung Chen, Chao-Hsi Lee, Jui-Hung Hung, Chia-Hsiang Yang   +5 more
semanticscholar   +1 more source

Parallelization of FM-Index

2008 10th IEEE International Conference on High Performance Computing and Communications, 2008
A parallel design and implementation of FM-index is presented in this paper. In applications, the performance of the FM-index is crucial, which is a self-contained, highly compressed indexing algorithm. With the popularity of multi-core processors, parallel computing allows the FM-index to run faster by performing multiple computations simultaneously ...
Di Zhang, Yunquan Zhang, Shengfei Liu, Xiaodi Huang 0001   +3 more
openaire   +1 more source

Relative FM-Indexes

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, Gagie, Travis, Gog, Simon, MANZINI, Giovanni, Sirén, Jouni   +4 more
openaire   +2 more sources