Results 31 to 40 of about 301,848 (186)
Sampling the Suffix Array with Minimizers [PDF]
, 2015 Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampling scheme allowing for more efficient pattern searches compared to the sparse suffix array, for long enough patterns.
Szymon Grabowski, Marcin Raniszewski
openaire +4 more sources
Gclust: A Parallel Clustering Tool for Microbial Genomic Data
Genomics, Proteomics & Bioinformatics, 2019 The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources. Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering ...
Ruilin Li +17 more
doaj +1 more source
On An Improved Parallel Construction Of Suffix Arrays For Low Bandwidth Pc-Cluster. [PDF]
, 2003 An algorithm for the parallel construction of suffix arrays generation for any texts with larger alphabet size on distributed memory architecture is ...
Md. Ali, Norhashidah +3 more
core +1 more source
Approximate String Matching with Compressed Indexes
Algorithms, 2009 A compressed full-text self-index for a text T is a data structure requiring reduced space and able to search for patterns P in T. It can also reproduce any substring of T, thus actually replacing T. Despite the recent explosion of interest on compressed
Pedro Morales +3 more
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Human Language Technologies 2007: The Conference of the North American Chapter of the Association for Computational Linguistics; Companion Volume, Short Papers on XX - NAACL '07, 2007 Suppose we have a large dictionary of strings. Each entry starts with a figure of merit (popularity). We wish to find the k-best matches for a substring, s, in a dictinoary, dict. That is, grep s dict | sort -n | head -k, but we would like to do this in sublinear time.
Kenneth Ward Church +2 more
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Variable-order reference-free variant discovery with the Burrows-Wheeler Transform
BMC Bioinformatics, 2020 Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision ...
Nicola Prezza +3 more
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Fast index based algorithms and software for matching position specific scoring matrices [PDF]
, 2006 Beckstette M, Homann R, Giegerich R, Kurtz S. Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics.
Kurtz Stefan +11 more
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Structator: fast index-based search for RNA sequence-structure patterns
BMC Bioinformatics, 2011 Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately,
Will Sebastian +4 more
doaj +1 more source
Relative Lempel-Ziv Compression of Suffix Arrays [PDF]
, 2020 We show that a combination of differential encoding, random sampling, and relative Lempel-Ziv (RLZ) parsing is effective for compressing suffix arrays, while simultaneously allowing very fast decompression of arbitrary suffix array intervals ...
Bella Zhukova +3 more
core +1 more source
Advanced Science, EarlyView.ProMetNet introduces a biologically constrained deep learning framework for proteo‐metabolomic integration by embedding Reactome‐derived pathway topology into neural networks. It captures non‐linear molecular dependencies and pathway‐level metabolic reorganization, enabling interpretable discrimination.
Minghui Zhao +6 more
wiley +1 more source