Results 11 to 20 of about 4,611,263 (171)
A Simple Alphabet-independent Fm-index [PDF]
International Journal of Foundations of Computer Science, 2006 We design a succinct full-text index based on the idea of Huffman-compressing the text and then applying the Burrows-Wheeler transform over it. The resulting structure can be searched as an FM-index, with the benefit of removing the sharp dependence on the alphabet size, σ, present in that structure.
S. Grabowski +4 more
semanticscholar +7 more sources
Simple Runs-Bounded FM-Index Designs Are Fast
The Sea, 2023 Peer ...
Diego Díaz-Domínguez +3 more
semanticscholar +5 more sources
FM-index of alignment: A compressed index for similar strings
Theoretical Computer Science, 2016 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
J. Na +6 more
semanticscholar +3 more sources
International Conference -Beyond Databases, Architectures, and Structures, 2015 The FM-index is a celebrated compressed data structure for full-text pattern searching. After the first wave of interest in its theoretical developments, we can observe a surge of interest in practical FM-index variants in the last few years.
S. Grabowski +2 more
semanticscholar +3 more sources
FM-Index Reveals the Reverse Suffix Array
Annual Symposium on Combinatorial Pattern Matching, 2020 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. The suffix array needs Θ(nlog n) bits of space compared to the n log σ bits needed to store T itself. A major breakthrough [FM - Index, FOCS'00] in the last two decades has been encoding the suffix array in near-optimal number of
Arnab Ganguly +6 more
semanticscholar +4 more sources
FM-Index on GPU: A Cooperative Scheme to Reduce Memory Footprint [PDF]
2014 IEEE International Symposium on Parallel and Distributed Processing with Applications, 2014 The FM-index is a data structure which is seeing more and more pervasive use, in particular in the field of high-throughput bioinformatics. Algorithms based on it show a pseudo-random memory access pattern.
Alejandro Chacón +4 more
semanticscholar +2 more sources
SPIRE, 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 ...
P. Ferragina +3 more
semanticscholar +4 more sources
Parallel Lightweight Wavelet Tree, Suffix Array and FM-Index Construction
2016 Data Compression Conference (DCC), 2016 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Julian Labeit, Julian Shun, G. Blelloch
semanticscholar +5 more sources
Efficient construction of an assembly string graph using the FM-index [PDF]
Bioinformatics, 2010 Motivation: Sequence assembly is a difficult problem whose importance has grown again recently as the cost of sequencing has dramatically dropped. Most new sequence assembly software has started by building a de Bruijn graph, avoiding the overlap-based ...
J. Simpson, R. Durbin
semanticscholar +3 more sources
Compressing Similar Biological Sequences Using FM-Index
2014 Data Compression Conference, 2014 Nowadays, 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
P. Procházka, J. Holub
semanticscholar +2 more sources