Results 1 to 10 of about 4,504,185 (191)

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, Luca Renders, Thomas Abeel, Jan Fostier   +3 more
doaj   +8 more sources

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

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

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   +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, James Holt, Leonard McMillan, Corbin D. Jones   +3 more
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, Oliva M, Köppl D, Bannai H, Boucher C, Gagie T.   +5 more
europepmc   +6 more sources

Pfp-fm: an accelerated FM-index [PDF]

Algorithms for Molecular Biology
FM-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, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie   +5 more
doaj   +3 more sources

PalFM-index: FM-index for Palindrome Pattern Matching [PDF]

Annual Symposium on Combinatorial Pattern Matching, 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

Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index

bioRxiv, 2018
Finding approximate occurrences of a pattern in a text using a full-text index is a central problem in bioinformatics and has been extensively researched.
Kianfar, Kiavash, Luo, Haochen, Pockrandt, Christopher, Reinert, Knut, Torkamandi, Bahman   +4 more
core   +2 more sources

Non-Linear Association Between Phase Angle and Body Fat in a Sample of US Adults [PDF]

Biology
Phase angle (PhA) is a widely used bioimpedance index associated with cell mass, membrane integrity, skeletal muscle mass and quality, and body fluid distribution.
Federica Frau, Eduardo Pizzo Junior, Stefano Cabras, Myosotis Massidda, Elisabetta Marini   +4 more
doaj   +2 more sources