Results 1 to 10 of about 4,611,263 (171)
An optimized FM-index library for nucleotide and amino acid search [PDF]
Algorithms for Molecular Biology, 2021 Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text ...
Tim Anderson, Travis J. Wheeler
doaj +7 more sources
Pan-genome de Bruijn graph using the bidirectional FM-index [PDF]
BMC Bioinformatics, 2023 Background Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, as their graph topology naturally ...
Lore Depuydt +3 more
doaj +8 more sources
An efficient error correction algorithm using FM-index [PDF]
BMC Bioinformatics, 2017 Background High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing.
Yao-Ting Huang, Yu-Wen Huang
doaj +6 more sources
PFP-FM: An Accelerated FM-index
Algorithms for Molecular Biology, 2023 FM-indexes are a crucial data structure in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern.
Hong A +5 more
europepmc +6 more sources
Pfp-fm: an accelerated FM-index [PDF]
Algorithms for Molecular BiologyFM-indexes are crucial data structures in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern.
Aaron Hong +5 more
doaj +3 more sources
Acceleration of FM-index Queries Through Prefix-free Parsing [PDF]
Algorithms Bioinform, 2023 FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [5] observed in 2007 that word-based indexes often use fewer
Hong A +5 more
europepmc +8 more sources
FMLRC: Hybrid long read error correction using an FM-index [PDF]
BMC Bioinformatics, 2018 Background Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the continuity and accuracy of genome ...
Jeremy R. Wang +3 more
doaj +3 more sources
Fast construction of FM-index for long sequence reads. [PDF]
Bioinformatics, 2014 SUMMARY We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse ...
Li H.
europepmc +7 more sources
PalFM-index: FM-index for Palindrome Pattern Matching [PDF]
CoRR, 2022 The palindrome pattern matching (pal-matching) is a kind of generalized pattern matching, in which two strings $x$ and $y$ of same length are considered to match (pal-match) if they have the same palindromic structures, i.e., for any possible $1 \le ...
Shinya Nagashita, I. Tomohiro
semanticscholar +5 more sources
FM-index of Alignment with Gaps [PDF]
Theoretical Computer Science, 2016 Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access.
J. Na +7 more
semanticscholar +5 more sources