Search Results - "Frith, Martin"

A simple method for finding related sequences by adding probabilities of alternative alignments by Frith, Martin C

“…The main way of analyzing genetic sequences is by finding sequence regions that are related to each other. There are many methods to do that, usually based on…”
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Adding unaligned sequences into an existing alignment using MAFFT and LAST by KATOH, Kazutaka, FRITH, Martin C

“…Two methods to add unaligned sequences into an existing multiple sequence alignment have been implemented as the '--add' and '--addfragments' options in the…”
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Minimally overlapping words for sequence similarity search by Frith, Martin C, Noé, Laurent, Kucherov, Gregory

“…Abstract Motivation Analysis of genetic sequences is usually based on finding similar parts of sequences, e.g. DNA reads and/or genomes. For big data, this is…”
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Improved DNA-Versus-Protein Homology Search for Protein Fossils by Yao, Yin, Frith, Martin C.

“…Protein fossils, i.e., noncoding DNA descended from coding DNA, arise frequently from transposable elements (TEs), decayed genes, and viral integrations. They…”
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Split-alignment of genomes finds orthologies more accurately by Frith, Martin C, Kawaguchi, Risa

“…We present a new pair-wise genome alignment method, based on a simple concept of finding an optimal set of local alignments. It gains accuracy by not masking…”
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new repeat-masking method enables specific detection of homologous sequences by Frith, Martin C

“…Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to…”
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How sequence alignment scores correspond to probability models by Frith, Martin C

“…Abstract Motivation Sequence alignment remains fundamental in bioinformatics. Pair-wise alignment is traditionally based on ad hoc scores for substitutions,…”
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DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development by Frith, Martin C, Ni, Shengliang

“…Abstract DNA that controls gene expression (e.g. enhancers, promoters) has seemed almost never to be conserved between distantly related animals, like…”
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Adaptive seeds tame genomic sequence comparison by Kiełbasa, Szymon M, Wan, Raymond, Sato, Kengo, Horton, Paul, Frith, Martin C

“…The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern…”
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Significant non-existence of sequences in genomes and proteomes by Koulouras, Grigorios, Frith, Martin C

“…Abstract Minimal absent words (MAWs) are minimal-length oligomers absent from a genome or proteome. Although some artificially synthesized MAWs have…”
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Parameters for accurate genome alignment by Frith, Martin C, Hamada, Michiaki, Horton, Paul

“…Genome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and…”
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Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements by Frith, Martin C.

“…Abstract Genomes hold a treasure trove of protein fossils: Fragments of formerly protein-coding DNA, which mainly come from transposable elements (TEs) or host…”
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lamassemble: Multiple Alignment and Consensus Sequence of Long Reads by Frith, Martin C, Mitsuhashi, Satomi, Katoh, Kazutaka

“…Long DNA and RNA reads from nanopore and PacBio technologies have many applications, but the raw reads have a substantial error rate. More accurate sequences…”
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Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease by Sone, Jun, Mitsuhashi, Satomi, Fujita, Atsushi, Mizuguchi, Takeshi, Hamanaka, Kohei, Mori, Keiko, Koike, Haruki, Hashiguchi, Akihiro, Takashima, Hiroshi, Sugiyama, Hiroshi, Kohno, Yutaka, Takiyama, Yoshihisa, Maeda, Kengo, Doi, Hiroshi, Koyano, Shigeru, Takeuchi, Hideyuki, Kawamoto, Michi, Kohara, Nobuo, Ando, Tetsuo, Ieda, Toshiaki, Kita, Yasushi, Kokubun, Norito, Tsuboi, Yoshio, Katoh, Kazutaka, Kino, Yoshihiro, Katsuno, Masahisa, Iwasaki, Yasushi, Yoshida, Mari, Tanaka, Fumiaki, Suzuki, Ikuo K., Frith, Martin C., Matsumoto, Naomichi, Sobue, Gen

“…Neuronal intranuclear inclusion disease (NIID) is a progressive neurodegenerative disease that is characterized by eosinophilic hyaline intranuclear inclusions…”
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Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads by Mitsuhashi, Satomi, Frith, Martin C, Mizuguchi, Takeshi, Miyatake, Satoko, Toyota, Tomoko, Adachi, Hiroaki, Oma, Yoko, Kino, Yoshihiro, Mitsuhashi, Hiroaki, Matsumoto, Naomichi

“…Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report…”
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Training alignment parameters for arbitrary sequencers with LAST-TRAIN by Hamada, Michiaki, Ono, Yukiteru, Asai, Kiyoshi, Frith, Martin C

“…LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions…”
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How to optimally sample a sequence for rapid analysis by Frith, Martin C, Shaw, Jim, Spouge, John L

“…We face an increasing flood of genetic sequence data, from diverse sources, requiring rapid computational analysis. Rapid analysis can be achieved by sampling…”
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A survey of localized sequence rearrangements in human DNA by Frith, Martin C, Khan, Sofia

“…Abstract Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what…”
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Discovering sequence motifs with arbitrary insertions and deletions by Frith, Martin C, Saunders, Neil F W, Kobe, Bostjan, Bailey, Timothy L

“…BIOLOGY IS ENCODED IN MOLECULAR SEQUENCES: deciphering this encoding remains a grand scientific challenge. Functional regions of DNA, RNA, and protein…”
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Mammalian NUMT insertion is non-random by Tsuji, Junko, Frith, Martin C, Tomii, Kentaro, Horton, Paul

“…It is well known that remnants of partial or whole copies of mitochondrial DNA, known as Nuclear MiTochondrial sequences (NUMTs), are found in nuclear genomes…”
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