Výsledky vyhledávání - "Sequence Alignment methods"

Using an integrative machine learning approach utilising homology modelling to clinically interpret genetic variants: CACNA1F as an exemplar: CACNA1F as an exemplar

Autoři: Simon C. Lovell Panagiotis I. Sergouniotis Rachel L. Taylor a další

Zdroj: Eur J Hum Genet
Sallah, S R, Sergouniotis, P I, Barton, S, Ramsden, S, Taylor, R L, Safadi, A, Kabir, M, Ellingford, J M, Lench, N, Lovell, S C & Black, G C M 2020, 'Using an integrative machine learning approach utilising homology modelling to clinically interpret genetic variants : CACNA1F as an exemplar', European Journal of Human Genetics, vol. 28, no. 9, pp. 1274-1282. https://doi.org/10.1038/s41431-020-0623-y

Témata: 0301 basic medicine, 0303 health sciences, Calcium Channels, L-Type, L-Type/chemistry, Protein, Calcium Channels, L-Type/chemistry, Sequence Alignment/methods, Sequence Analysis, DNA, Article, DNA/methods, Machine Learning, 03 medical and health sciences, Sequence Analysis, DNA/methods, Structural Homology, Protein, Mutation, Animals, Humans, Calcium Channels, Genetic Testing, Sequence Analysis, Sequence Alignment, Genetic Testing/methods, Structural Homology

Přístupová URL adresa: https://www.nature.com/articles/s41431-020-0623-y.pdf
https://pubmed.ncbi.nlm.nih.gov/32313206
https://research.manchester.ac.uk/en/publications/f87a43f7-3c53-4a5b-a60d-85b2d0fb18ce
https://doi.org/10.1038/s41431-020-0623-y
https://www.nature.com/articles/s41431-020-0623-y.pdf
https://pubmed.ncbi.nlm.nih.gov/32313206/
https://www.nature.com/articles/s41431-020-0623-y
https://www.research.manchester.ac.uk/portal/en/publications/using-an-integrative-machine-learning-approach-utilising-homology-modelling-to-clinically-interpret-genetic-variants-cacna1f-as-an-exemplar(f87a43f7-3c53-4a5b-a60d-85b2d0fb18ce).html
https://europepmc.org/article/PMC/PMC7608274
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608274

Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics.

Autoři: Collyn, F. Guy, L. Marceau, M. a další

Témata: Chromosome Mapping/methods, Evolution, Molecular, Gene Transfer, Horizontal/genetics, Genome, Bacterial, Genomic Islands/genetics, Nucleotides/genetics, Phylogeny, Sequence Alignment/methods, Sequence Analysis, DNA/methods, Virulence Factors/genetics, Yersinia/genetics

Popis souboru: application/pdf

Relation: Bioinformatics; 1367-4803[print], 1367-4803[linking]; https://iris.unil.ch/handle/iris/49399; serval:BIB_4CBE419539E7; 000236997600006

Dostupnost: https://iris.unil.ch/handle/iris/49399
https://doi.org/10.1093/bioinformatics/bti793

Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.

Autoři: Poirot, O. O'Toole, E. Notredame, C.

Témata: Consensus Sequence, Internet, Phylogeny, Sequence Alignment/methods, Sequence Analysis, DNA/methods, Protein/methods, RNA/methods, Software

Relation: Nucleic Acids Research; 1362-4962[electronic]; https://iris.unil.ch/handle/iris/128434; serval:BIB_27597; 000183832900046

Dostupnost: https://iris.unil.ch/handle/iris/128434
https://doi.org/10.1093/nar/gkg522

Zoledronic Acid Induces Site-Specific Structural Changes and Decreases Vascular Area in the Alveolar Bone

Autoři: Silveira Soares, Mariana Quirino Van Dessel, Jeroen Jacobs, Reinhilde a další

Zdroj: Journal of Oral and Maxillofacial Surgery. 76:1893-1901

Témata: Male, 0301 basic medicine, MICRODAMAGE ACCUMULATION, 1105 Dentistry, OSTEOPOROSIS, MICRO-CT, THERAPY, Zoledronic Acid, 03 medical and health sciences, Imaging, Three-Dimensional, 0302 clinical medicine, 3203 Dentistry, Bone Density, Dentistry, Oral Surgery & Medicine, RAT MODEL, Alveolar Process, Animals, Activity-based model, validation, sequence alignment methods, classification methods, process models, ALBATROSS, Rats, Wistar, ALENDRONATE, Science & Technology, TRABECULAR BONE, HISTOMORPHOMETRY, X-Ray Microtomography, Rats, 3. Good health, JAW, Dentistry, BIOMECHANICAL PROPERTIES, RISK-FACTORS, TURNOVER, Bisphosphonate-Associated Osteonecrosis of the Jaw, BISPHOSPHONATE-RELATED OSTEONECROSIS, Life Sciences & Biomedicine, DOG RIB, MICROARCHITECTURE

Popis souboru: application/pdf

Přístupová URL adresa: http://www.joms.org/article/S0278239118302209/pdf
https://pubmed.ncbi.nlm.nih.gov/29626448
https://www.sciencedirect.com/science/article/pii/S0278239118302209
https://europepmc.org/article/MED/29626448
https://pubmed.ncbi.nlm.nih.gov/29626448/
https://www.ncbi.nlm.nih.gov/pubmed/29626448
http://hdl.handle.net/1942/28498

Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability

Autoři: Fraser, Nicholas J. Liu, Jian-Wei Mabbitt, Peter D. a další

Zdroj: Journal of Molecular Biology. 428:2359-2371

Témata: 0301 basic medicine, Protein Structure, 0303 health sciences, Sheep, Mutation/genetics, Sequence Alignment/methods, Australia, Proteins, Protein Multimerization/genetics, Biological Evolution, Quaternary, 03 medical and health sciences, Proteins/genetics, Mutation, Sheep/genetics, Animals, Amino Acid Sequence, Protein Multimerization, Protein Structure, Quaternary, Sequence Alignment

Přístupová URL adresa: http://manuscript.elsevier.com/S002228361600200X/pdf/S002228361600200X.pdf
https://pubmed.ncbi.nlm.nih.gov/27016206
http://www.sciencedirect.com/science/article/pii/S002228361600200X
https://europepmc.org/abstract/MED/27016206
https://www.ncbi.nlm.nih.gov/pubmed/27016206
https://discovery.dundee.ac.uk/en/publications/evolution-of-protein-quaternary-structure-in-response-to-selectiv
https://pubmed.ncbi.nlm.nih.gov/27016206/
https://www.rcsb.org/structure/5ikx

Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide–Rich Environments

Autoři: Kelley, Joanna L Arias-Rodriguez, Lenin Patacsil Martin, Dorrelyn a další

Zdroj: Mol Biol Evol
Molecular Biology and Evolution, vol 33, iss 6

Témata: ecological physiology, Acclimatization, Evolutionary biology, extreme environments, Hydrogen Sulfide - metabolism, Hydrogen Sulfide, Physiological - genetics, Genome, H2S, Biological Sciences, Sequence Alignment - methods, Adaptation, Physiological, Biological Evolution, Sequence Analysis, Biotechnology, Gene Flow, Evolution, Physiological, Population, RNA-sequencing, Poecilia - physiology, Environment, RNA - methods, Physiological - physiology, Evolution, Molecular, Genetic, evolution, Acclimatization - physiology, Genetics, Animals, 14. Life underwater, Adaptation, Selection, Genetic, Population - methods, Selection, Discoveries, Ecosystem, Acclimatization - genetics, Evolutionary Biology, Poecilia, Sequence Analysis, RNA, Human Genome, Molecular, Poecilia - genetics, Poecilia mexicana, Genetics, Population, 13. Climate action, Biochemistry and cell biology, gene expression, Poecilia - metabolism, RNA, Biochemistry and Cell Biology, Transcriptome, Sequence Alignment

Popis souboru: application/pdf; pdf

Přístupová URL adresa: https://academic.oup.com/mbe/article-pdf/33/6/1419/17471144/msw020.pdf
https://pubmed.ncbi.nlm.nih.gov/26861137
http://europepmc.org/abstract/MED/26861137
https://pubmed.ncbi.nlm.nih.gov/26861137/
https://paperity.org/p/76052555/mechanisms-underlying-adaptation-to-life-in-hydrogen-sulfide-rich-environments
https://academic.oup.com/mbe/article/33/6/1419/2579358
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868117/
https://escholarship.org/content/qt9q21807t/qt9q21807t.pdf
https://escholarship.org/uc/item/9q21807t

Characterizing activity sequences using profile Hidden Markov Models

Autoři: Liu, Feng Janssens, Davy Cui, JianXun a další

Přispěvatelé: Liu, Feng Janssens, Davy Cui, JianXun a další

Zdroj: Expert Systems with Applications. 42:5705-5722

Témata: Business & economic sciences, Special economic topics (health, labor, transportation...), multiple sequence alignments, Activity sequences, profile Hidden Markov Models (pHMMs), 05 social sciences, Activity-travel diaries, Mobile phone data, 02 engineering and technology, 16. Peace & justice, Engineering, computing & technology, Ingénierie, informatique & technologie, 3. Good health, Domaines particuliers de l'économie (santé, travail, transport...), Ingénierie civile, 0502 economics and business, 0202 electrical engineering, electronic engineering, information engineering, Sequence Alignment Methods (SAM), Civil engineering, Sciences économiques & de gestion

MANTIS: a phylogenetic framework for multi-species genome comparisons

Autoři: Tzika, Athanasia Helaers, Raphaël Van de peer, Yves a další

Přispěvatelé: Tzika, Athanasia Helaers, Raphaël Van de peer, Yves a další

Zdroj: Bioinformatics (Oxford, England), Vol. 24, no. 2, p. 151-157 (2008)
BIOINFORMATICS

Témata: SELECTION, 0301 basic medicine, Chromosome Mapping -- methods, Biochimie, Molecular Sequence Data, Informatique appliquée logiciel, comparative genomics, Chromosome Mapping - methods, ANNOTATION, Databases, User-Computer Interface, 03 medical and health sciences, Genetic, Informatique mathématique, Databases, Genetic, Computer Graphics, PRESERVATION, Statistique mathématique, ancestral genomes, SUBFUNCTIONALIZATION, Phylogeny, NEOFUNCTIONALIZATION, 0303 health sciences, multi-species comparisons, Base Sequence, Sequence Analysis, DNA - methods, DNA -- methods, Biologie moléculaire, Biology and Life Sciences, Chromosome Mapping, phylogenomics, Probabilités, Sequence Analysis, DNA, Sequence Alignment - methods, EVOLUTION, Sequence Alignment -- methods, DUPLICATE GENES, Database Management Systems, INFERENCE, Sequence Analysis, Sequence Alignment, SYSTEM, Software

Popis souboru: application/pdf; 2 full-text file(s): application/pdf

Přístupová URL adresa: https://academic.oup.com/bioinformatics/article-pdf/24/2/151/16883181/btm567.pdf
https://pubmed.ncbi.nlm.nih.gov/18025004
https://researchportal.unamur.be/en/publications/370a6a85-a67a-4eb2-9494-eb16a13c04ba
https://hdl.handle.net/2078/71411
http://hdl.handle.net/1854/LU-417304
http://doi.org/10.1093/bioinformatics/btm567
https://biblio.ugent.be/publication/417304/file/3065650
https://biblio.ugent.be/publication/417304

Structural Alignment of RNA with Triple Helix Structure

Autoři: Yiu, SM Wong, TKF

Zdroj: Journal of Computational Biology. 19:365-378

Témata: Models, Molecular, 0301 basic medicine, RNA, Untranslated, Base Sequence, Sequence Analysis, RNA, 0206 medical engineering, Untranslated - chemistry, 02 engineering and technology, RNA - methods, Sequence Alignment - methods, 03 medical and health sciences, RNA, Untranslated - chemistry, RNA, Nucleic Acid Conformation, Sequence Analysis, Sequence Alignment, Sequence Analysis, RNA - methods, Algorithms

Přístupová URL adresa: http://hub.hku.hk/bitstream/10722/165843/1/Content.pdf
https://pubmed.ncbi.nlm.nih.gov/22468707
http://www.liebertpub.com/doi/10.1089/cmb.2010.0052
https://pubmed.ncbi.nlm.nih.gov/22468707/
https://dblp.uni-trier.de/db/journals/jcb/jcb19.html#WongY12
https://core.ac.uk/display/37987956
http://hub.hku.hk/bitstream/10722/165843/1/Content.pdf
http://hub.hku.hk/handle/10722/165843
http://hdl.handle.net/10722/165843

Evaluation of DNA Mixtures from Database Search

Autoři: Fung, WK Chung, YK Hu, YQ

Zdroj: Chung, Y K, Hu, Y & Fung, W-K 2010, 'Evaluation of DNA Mixtures from Database Search', Biometrics, vol. 66, no. 1, pp. 233-238. https://doi.org/10.1111/j.1541-0420.2009.01271.x

Témata: Forensic Genetics, likelihood ratio, Database search, Molecular Sequence Data, Information Storage and Retrieval, Sequence Analysis, Dna - Methods, database search, Databases, 03 medical and health sciences, 0302 clinical medicine, Genetic, Information Storage And Retrieval - Methods, Databases, Genetic, Mixture, Dna - Genetics, Humans, Dna - Methods, Forensic Genetics - Methods, Base Sequence, DNA, Sequence Analysis, DNA, Likelihood ratio, mixture, Sequence Alignment - Methods, Database Management Systems, Sequence Analysis, Sequence Alignment

Přístupová URL adresa: https://pubmed.ncbi.nlm.nih.gov/19459834
https://research.manchester.ac.uk/en/publications/11ce21b8-76b4-48db-b025-50d03555ac8d
https://doi.org/10.1111/j.1541-0420.2009.01271.x
https://www.ncbi.nlm.nih.gov/pubmed/19459834
http://hub.hku.hk/handle/10722/172470
https://EconPapers.repec.org/RePEc:bla:biomet:v:66:y:2010:i:1:p:233-238
https://jglobal.jst.go.jp/en/detail?JGLOBAL_ID=201002275867985702
https://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2009.01271.x
http://hdl.handle.net/10722/172470

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

Autoři: Lu, David V Brown, Randall H Arumugam, Manimozhiyan a další

Zdroj: Bioinformatics. 25:1587-1593

Témata: 0301 basic medicine, DNA, Complementary, Genomics: methods, Base Sequence, Complementary: chemistry, 0206 medical engineering, DNA, Genomics, 02 engineering and technology, Markov Chains, Rats, Mice, 03 medical and health sciences, Complementary, Animals, Humans, Sequence Alignment: methods, Sequence Alignment

Přístupová URL adresa: https://academic.oup.com/bioinformatics/article-pdf/25/13/1587/16887648/btp273.pdf
https://pubmed.ncbi.nlm.nih.gov/19414532

A Highly Conserved Motif within the NH2-terminal Coiled-coil Domain of Angiopoietin-like Protein 4 Confers Its Inhibitory Effects on Lipoprotein Lipase by Disrupting the Enzyme Dimerization

Autoři: Wang, Y Xu, A Yau, MH a další

Zdroj: Journal of Biological Chemistry. 284:11942-11952

Témata: 0301 basic medicine, Protein Structure, Amino Acid Motifs, Tertiary - Physiology, Peptide Mapping, Lipoprotein Lipase - Antagonists & Inhibitors - Genetics - Metabolism, Enzyme Inhibitors - Metabolism, Mice, 03 medical and health sciences, 3T3-L1 Cells, Angiopoietin-Like Protein 4, Animals, Humans, Amino Acid Motifs - Physiology, Enzyme Inhibitors, Angiopoietin-Like Protein 3, 0303 health sciences, Angiopoietins - Genetics - Metabolism, Protein Structure, Tertiary - Physiology, Protein Structure, Tertiary, Lipoprotein Lipase, Angiopoietin-like Proteins, Amino Acid Substitution, Sequence Alignment - Methods, Mutation, Peptide Mapping - Methods, Angiopoietins, Dimerization, Sequence Alignment

Přístupová URL adresa: http://www.jbc.org/content/284/18/11942.full.pdf
https://pubmed.ncbi.nlm.nih.gov/19246456
https://www.sciencedirect.com/science/article/pii/S0021925820583543
https://europepmc.org/article/MED/19246456
http://www.jbc.org/content/284/18/11942.abstract
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673263/
https://hub.hku.hk/handle/10722/163249
http://intl.jbc.org/cgi/reprint/284/18/11942.pdf
http://hdl.handle.net/10722/163249

R-Coffee: a web server for accurately aligning noncoding RNA sequences

Autoři: Moretti, Sébastien Wilm, Andreas Higgins, Desmond G. a další

Zdroj: Nucleic Acids Res
Nucleic Acids Research, vol. 36, no. Web Server issue, pp. W10-W13

Témata: 0301 basic medicine, Internet, 0303 health sciences, 03 medical and health sciences, RNA, Untranslated, Sequence Analysis, RNA, Algorithms, Nucleic Acid Conformation, RNA, Untranslated/chemistry, Sequence Alignment/methods, Software, Articles, Sequence Alignment

Popis souboru: application/pdf

Přístupová URL adresa: https://academic.oup.com/nar/article-pdf/36/suppl_2/W10/7627355/gkn278.pdf
https://pubmed.ncbi.nlm.nih.gov/18483080
https://serval.unil.ch/resource/serval:BIB_D39CC5C415A8.P001/REF.pdf
http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_D39CC5C415A80
https://serval.unil.ch/notice/serval:BIB_D39CC5C415A8
http://doc.rero.ch/record/294141/files/gkn278.pdf

Compressed indexing and local alignment of DNA

Autoři: Lam, T.W. Sung, W.K. Tam, S.L. a další

Přispěvatelé: Lam, T.W. Sung, W.K. Tam, S.L. a další

Zdroj: Bioinformatics. 24:791-797

Témata: DNA - methods, 0301 basic medicine, Genome, Base Sequence, Genome, Human, Sequence Analysis, DNA - methods, Molecular Sequence Data, 0206 medical engineering, DNA - genetics, Data Compression - methods, Chromosome Mapping, Human - genetics, DNA, Sequence Analysis, DNA, 02 engineering and technology, Chromosome Mapping - methods, Sequence Alignment - methods, Data Compression, 03 medical and health sciences, Humans, Sequence Analysis, Genome, Human - genetics, Sequence Alignment, Algorithms

Přístupová URL adresa: https://academic.oup.com/bioinformatics/article-pdf/24/6/791/16886605/btn032.pdf
https://pubmed.ncbi.nlm.nih.gov/18227115
http://hdl.handle.net/10722/89140

Remote homology detection of integral membrane proteins using conserved sequence features

Autoři: Bernsel, Andreas Viklund, Håkan Elofsson, Arne

Zdroj: Proteins. 71(3):1387-1399

Témata: Conserved Sequence, Databases, Protein, Hydrophobicity, Markov Chains, Membrane Proteins/*chemistry, Sensitivity and Specificity, Sequence Alignment/*methods, Sequence Analysis, Protein/methods, Sequence Homology, Amino Acid

Popis souboru: print

Přístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-14855

Finding motifs from all sequences with and without binding sites

Autoři: Chin, FYL Leung, HCM

Zdroj: Bioinformatics. 22:2217-2223

Témata: 0301 basic medicine, Genetic - genetics, Amino Acid Motifs, Molecular Sequence Data, 0206 medical engineering, 02 engineering and technology, Promoter Regions, 03 medical and health sciences, Models, Promoter Regions, Genetic, DNA - methods, Binding Sites, Models, Statistical, Base Sequence, Transcription Factors - chemistry - genetics - metabolism, Sequence Analysis, DNA - methods, Sequence Analysis, DNA, Statistical, Sequence Alignment - methods, Promoter Regions, Genetic - genetics, Sequence Analysis, Sequence Alignment, Algorithms, Protein Binding, Transcription Factors

Přístupová URL adresa: https://academic.oup.com/bioinformatics/article-pdf/22/18/2217/901881/btl371.pdf
https://pubmed.ncbi.nlm.nih.gov/16870937
http://hdl.handle.net/10722/88894

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.

Autoři: Lassmann, Timo Sonnhammer, Erik L L

Zdroj: Nucleic Acids Res. 34(Web Server issue):W596-9

Témata: Internet, Quality Control, Sequence Alignment/*methods/standards, Sequence Analysis, Protein, Software, User-Computer Interface

Popis souboru: print

Přístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-21056

Prediction of function divergence in protein families using the substitution rate variation parameter alpha.

Autoři: Abhiman, Saraswathi Daub, Carsten O Sonnhammer, Erik L L

Zdroj: Mol Biol Evol. 23(7):1406-13

Témata: Algorithms, Amino Acid Substitution/*genetics, Computational Biology/*methods, Conserved Sequence/genetics, Evolution, Molecular, Phylogeny, Proteins/*genetics/physiology, Reproducibility of Results, Sequence Alignment/methods, Variation (Genetics)/*genetics

Popis souboru: print

Přístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-21057

Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

Autoři: Alexeyenko, Andrey Tamas, Ivica Liu, Gang a další

Zdroj: Bioinformatics. 22(14):e9-15

Témata: Algorithms, Animals, Artificial Intelligence, Cluster Analysis, Conserved Sequence/genetics, Evolution, Molecular, Humans, Pattern Recognition, Automated/methods, Phylogeny, Proteome/*genetics, Sequence Alignment/*methods, Sequence Analysis, DNA/*methods, Sequence Homology, Amino Acid

Popis souboru: print

Přístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-21066

FoldIndex(C): a simple tool to predict whether a given protein sequence is intrinsically unfolded

Autoři: Prilusky, Jaime Felder, Clifford E. Zeev-Ben-Mordehai, Tzviya a další

Zdroj: Bioinformatics, vol. 21, no. 16, pp. 3435-8

Témata: Models, Molecular, 0301 basic medicine, Internet, Protein Folding, 0303 health sciences, Protein Conformation, Proteins, Structure-Activity Relationship, User-Computer Interface, 03 medical and health sciences, Energy Transfer, Models, Chemical, Sequence Analysis, Protein, Algorithms Computer Graphics Computer Simulation Energy Transfer Internet *Models, Chemical *Models, Molecular Protein Conformation Protein Folding Proteins/analysis/*chemistry Sequence Alignment/*methods Sequence Analysis, Protein/*methods *Software Structure-Activity Relationship *User-Computer Interface, Computer Graphics, Computer Simulation, Sequence Alignment, Algorithms, Software

Popis souboru: application/pdf

Přístupová URL adresa: https://academic.oup.com/bioinformatics/article-pdf/21/16/3435/571946/bti537.pdf
https://pubmed.ncbi.nlm.nih.gov/15955783
https://serval.unil.ch/resource/serval:BIB_072223A553B5.P001/REF.pdf
http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_072223A553B58
https://serval.unil.ch/notice/serval:BIB_072223A553B5
https://dspace.library.uu.nl/handle/1874/357755
http://doc.rero.ch/record/303357/files/bti537.pdf