Sökresultat - "sequence alignment"

MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.

Patsakis M; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Provatas K; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Karatzikos A; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Koilakos C; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Mouratidis I; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA. ioannis.mouratidis@psu.edu.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA. ioannis.mouratidis@psu.edu., Georgakopoulos-Soares I; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA. izg5139@psu.edu.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA. izg5139@psu.edu.

Journal Article , 2025

Fast noisy long read alignment with multi-level parallelism.

Xia Z; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Yang C; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China.; National Supercomputer Center in Tianjin, 300457, Tianjin, China.; Haihe Lab of ITAI, 300457, Tianjin, China., Peng C; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Guo Y; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Guo Y; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Tang T; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Cui Y; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China. yingbocui@nudt.edu.cn.

Journal Article , 2025

Assessment of bisulfite sequencing alignment tools for whole genome analysis in plants.

Wu Q; National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China., Yang M; Qionghai Tropical Crops Service Center, Qionghai 571400, China., Yang Y; National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China., Iqbal A; Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; Department of Food Science & Technology, Abdul Wali Khan University Mardan, Pakistan., Zhou L; National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China. Electronic address: lxzhou@catas.cn.

Journal Article , 2025

Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments.

Holtgrefe N; Delft Institute of Applied Mathematics, Delft University of Technology, Mekelweg 4, Delft 2628 CD, The Netherlands., Huber KT; School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK., van Iersel L; Delft Institute of Applied Mathematics, Delft University of Technology, Mekelweg 4, Delft 2628 CD, The Netherlands., Jones M; Delft Institute of Applied Mathematics, Delft University of Technology, Mekelweg 4, Delft 2628 CD, The Netherlands., Martin S; European Bioinformatics Institute, Hinxton CB10 1SD, UK., Moulton V; School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

Journal Article , 2025

Blastn2dotplots: multiple dot-plot visualizer for genome comparisons.

Okuno M; Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, 830-0011, Japan. okuno_miki@med.kurume-u.ac.jp., Yamamoto T; Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, 830-0011, Japan., Ogura Y; Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, 830-0011, Japan.

Journal Article , 2025

epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum assignment problem formulation.

Zhang X; Department of Electronic and Computational Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China., Chen Z; Data Science and Analytics Thrust, Information Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China., Li J; Department of Ocean Science and Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong SAR, China., Luo Q; Data Science and Analytics Thrust, Information Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China.; Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China., Wu L; Department of Ocean Science and Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong SAR, China., Yu W; Department of Electronic and Computational Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.

Journal Article , 2025

TarP: A microRNA target gene prediction tool utilizing a polymorphic structured alignment approach.

Fan T; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China., Su Z; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China., Wang X; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China., Wei T; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China., Zhao L; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China., Liu S; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China. Electronic address: lspsm@swu.edu.cn.

Journal Article , 2025

Fast sequence alignment for centromeres with RaMA.

Zhang P; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, Zhejiang, China., Wei Y; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, Zhejiang, China.; School of Computer Science and Technology, Xidian University, Xi'an 710126, Shaanxi, China., Tian Q; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, Zhejiang, China., Zou Q; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, Zhejiang, China., Wang Y; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China; wangyansu@uestc.edu.cn.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, Zhejiang, China.

Journal Article , 2025

ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction.

Shao J, Chen J, Liu B

Journal Article; Research Support, Non-U.S. Gov't , 2025

K-mer analysis of long-read alignment pileups for structural variant genotyping.

English AC; Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA. Adam.English@bcm.edu., Cunial F; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Metcalf GA; Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA., Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Sedlazeck FJ; Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.; Department of Computer Science, Rice University, Houston, TX, USA.

Journal Article , 2025

Adaptive sequence alignment for metagenomic data analysis.

Pietilä S; Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland., Suomi T; Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland., Paulin N; Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland., Laiho A; Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland., Sclivagnotis YS; Orion Corporation, FI-20380, Turku, Finland., Elo LL; Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland. Electronic address: laura.elo@utu.fi.

Journal Article , 2025

X-Mapper: fast and accurate sequence alignment via gapped x-mers.

Gaston JM; Google, Cambridge, MA, USA.; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore., Alm EJ; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. ejalm@MIT.EDU., Zhang AN; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. anni.zhang@ntu.edu.sg.; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. anni.zhang@ntu.edu.sg.

Journal Article , 2025

PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.

Halpin JC; Department of Biology, MIT, Cambridge, Massachusetts, USA., Keating AE; Department of Biology, MIT, Cambridge, Massachusetts, USA.; Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA.; Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.

Journal Article , 2025

MAFin: motif detection in multiple alignment files.

Patsakis M; Institute for Personalized Medicine, Department of Molecular and Precision Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, United States., Provatas K; Institute for Personalized Medicine, Department of Molecular and Precision Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, United States.; Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece., Baltoumas FA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece., Chantzi N; Institute for Personalized Medicine, Department of Molecular and Precision Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, United States., Mouratidis I; Institute for Personalized Medicine, Department of Molecular and Precision Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, United States., Pavlopoulos GA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece., Georgakopoulos-Soares I; Institute for Personalized Medicine, Department of Molecular and Precision Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, United States.

Journal Article , 2025

wgatools: an ultrafast toolkit for manipulating whole-genome alignments.

Wei W; School of Life Sciences, Westlake University, Hangzhou 310030, China.; National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China., Gui S; National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China., Yang J; School of Life Sciences, Westlake University, Hangzhou 310030, China.; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China., Garrison E; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, United States., Yan J; National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China., Liu HJ; Yazhouwan National Laboratory, Sanya 572024, China.

Journal Article , 2025

Protocol for sequence clustering with PaSiMap in Jalview.

Morell T; Department of Biology, University of Konstanz, 78457 Konstanz, Germany., Procter J; Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee DD1 5EH, Scotland., Barton GJ; Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee DD1 5EH, Scotland., Diederichs K; Department of Biology, University of Konstanz, 78457 Konstanz, Germany., Mayans O; Department of Biology, University of Konstanz, 78457 Konstanz, Germany., Fleming JR; Department of Biology, University of Konstanz, 78457 Konstanz, Germany. Electronic address: jfleming@ebi.ac.uk.

Journal Article , 2025

FPGA-based accelerator for adaptive banded event alignment in nanopore sequencing data analysis.

Feng Y; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA. ypf5071@psu.edu., Li Z; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA., Gudukbay Akbulut G; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA., Narayanan V; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA., Kandemir MT; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA., Das CR; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA.

Journal Article , 2025

Generating multiple alignments on a pangenomic scale.

Olbrich J; Institute of Theoretical Computer Science, Ulm University, Ulm, 89069, Germany., Büchler T; Institute of Theoretical Computer Science, Ulm University, Ulm, 89069, Germany., Ohlebusch E; Institute of Theoretical Computer Science, Ulm University, Ulm, 89069, Germany.

Journal Article , 2025

QuickEd: high-performance exact sequence alignment based on bound-and-align.

Doblas M; Computer Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain.; Department of Computer Architecture, Universitat Politècnica de Catalunya Barcelona 08034, Spain., Lostes-Cazorla O; Computer Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain.; Department of Electronic Engineering, Universitat Politècnica de Catalunya, Barcelona 08034, Spain., Aguado-Puig Q; Computer Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain.; Department of Electronic Engineering, Universitat Politècnica de Catalunya, Barcelona 08034, Spain.; Department of Computer Architecture and Operative Systems, Universitat Autònoma de Barcelona, Barcelona 08193, Spain., Iñiguez C; Computer Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain., Moreto M; Computer Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain.; Department of Computer Architecture, Universitat Politècnica de Catalunya Barcelona 08034, Spain., Marco-Sola S; Computer Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain.; Department of Computer Science, Universitat Politècnica de Catalunya, Barcelona 08034, Spain.

Journal Article , 2025

TrAGEDy-trajectory alignment of gene expression dynamics.

Laidlaw RF; Centre for Parasitology, University of Glasgow, Glasgow, G12 8QQ, United Kingdom., Briggs EM; Centre for Parasitology, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.; Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, EH8 9YL, United Kingdom.; Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom., Matthews KR; Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, EH8 9YL, United Kingdom., Madany Mamlouk A; Institute for Neuro- and Bioinformatics, University of Lübeck, Lübeck, 23562, Germany., McCulloch R; Centre for Parasitology, University of Glasgow, Glasgow, G12 8QQ, United Kingdom., Otto TD; Centre for Parasitology, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.; Laboratory of Pathogens and Host Immunity, Universite de Montpellier, Montpellier, 34090, France.

Journal Article , 2025