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Start Over Author "Alexander Kanapin" Publisher oxford university press (oup)
6 results on '"Alexander Kanapin"'

1. Pygenomics: manipulating genomic intervals and data files in Python

Author

Gaik Tamazian, Nikolay Cherkasov, Alexander Kanapin, and Anastasia Samsonova

Subjects
Statistics and Probability, Computational Mathematics, Computational Theory and Mathematics, Molecular Biology, Biochemistry, Computer Science Applications
Abstract

Summary We present pygenomics, a Python package for working with genomic intervals and bioinformatic data files. The package implements interval operations, provides both API and CLI, and supports reading and writing data in widely used bioinformatic formats, including BAM, BED, GFF3 and VCF. The source code of pygenomics is provided with in-source documentation and type annotations and adheres to the functional programming paradigm. These features facilitate seamless integration of pygenomics routines into scripts and pipelines. The package is implemented in pure Python using its standard library only and contains the property-based testing framework. Comparison of pygenomics with other Python bioinformatic packages with relation to features and performance is presented. The performance comparison covers operations with genomic intervals, read alignments, and genomic variants and demonstrates that pygenomics is suitable for computationally effective analysis. Availability and Implementation The source code is available at https://gitlab.com/gtamazian/pygenomics. Supplementary information Supplementary data are available at Bioinformatics online. more...

Published
2023
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2. Reactome knowledgebase of human biological pathways and processes

Author

David B. Croft, Ewan Birney, Esther Schmidt, Alexander Kanapin, Henning Hermjakob, Lisa Matthews, Guanming Wu, Lincoln Stein, Imre Vastrik, Shahana S. Mahajan, Marc Gillespie, Phani V. Garapati, Peter D'Eustachio, Bijay Jassal, Michael Caudy, Bruce May, Suzanna E. Lewis, Gopal Gopinath, Bernard de Bono, and Jill Hemish more...

Subjects
animal structures, Computational biology, Biology, Bioinformatics, Biological pathway, 03 medical and health sciences, 0302 clinical medicine, Prediction methods, Genetics, Animals, Humans, Data content, Databases, Protein, Human proteins, Physiological Phenomena, Physiological Phenomenon, 030304 developmental biology, 0303 health sciences, Extramural, Proteins, Articles, Systems Integration, ComputingMethodologies_PATTERNRECOGNITION, Open source, 030220 oncology & carcinogenesis, Proteins metabolism, Models, Animal, Metabolic Networks and Pathways, Software, Signal Transduction
Abstract

Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms. more...

Published
2009
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3. New developments in the InterPro database

Author

David Lonsdale, Rodrigo Lopez, Rolf Apweiler, Richard R. Copley, Emmanuel Courcelle, Robert Petryszak, Alberto Labarga, Alex Bateman, Jennifer McDowall, Anastasia N. Nikolskaya, Christine A. Orengo, Nicolas Hulo, Martin Madera, Franck Valentin, Daniel H. Haft, Robert D. Finn, David Binns, Petra S. Langendijk-Genevaux, Ujjwal Das, Nicola Mulder, Louise C. Daugherty, Anish Kejariwal, Julian Gough, Virginie Buillard, Wolfgang Fleischmann, Amos Marc Bairoch, Daniel Kahn, Mark Dibley, Peer Bork, Craig McAnulla, Teresa K. Attwood, Cathy H. Wu, Lorenzo Cerutti, Alexander Kanapin, Christian J. A. Sigrist, John Maslen, Corin Yeats, Sarah Hunter, Paul Thomas, Ivica Letunic, Derek Wilson, Jaina Mistry, Sandra Orchard, Alex L. Mitchell, Jeremy D. Selengut, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Computer science and genomics (HELIX), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS) more...

Subjects
InterPro, Protein Structure, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Web server, computer.internet_protocol, Biology, PROSITE, computer.software_genre, Databases, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, Sequence Analysis, Protein, TIGRFAMs, Genetics, ddc:576, Databases, Protein, 030304 developmental biology, Internet, 0303 health sciences, Database, Protein, Proteins, Articles, Protein Structure, Tertiary, Systems Integration, Cardiovascular and Metabolic Diseases, [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], 030220 oncology & carcinogenesis, Proteins/chemistry/classification/physiology, Web service, UniProt, Sequence Analysis, computer, Tertiary, XML, Autre (Sciences du Vivant), InterProScan
Abstract

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html. more...

Published
2007
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4. The InterPro Database, 2003 brings increased coverage and new features

Author

Emmanuel Courcelle, Teresa K. Attwood, Evgeny M. Zdobnov, Nicolas Hulo, Sandra Orchard, Chris P. Ponting, Margaret Biswas, Sam Griffiths-Jones, Paul Bradley, Ivica Letunic, Robert M. Vaughan, David M. Lonsdale, Richard R. Copley, Marco Pagni, Rodrigo Lopez, Daniel H. Haft, Peer Bork, Jeremy D. Selengut, Nicola Mulder, Ujjwal Das, Wolfgang Fleischmann, Richard Durbin, Laurent Falquet, Rolf Apweiler, Phillip Bucher, Florence Servant, Ville Silventoinen, Alexander Kanapin, Alex Bateman, David Peyruc, Nicola Harte, Christian J. A. Sigrist, Daniel Barrell, Amos Marc Bairoch, Daniel Kahn, David Binns, Maria Krestyaninova, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Bairoch, Amos Marc, Falquet, Laurent, Hulo, Nicolas, Zdobnov, Evgeny, and MDC Library more...

Subjects
Proteins/chemistry/genetics/metabolism, Repetitive Sequences, Amino Acid, 0106 biological sciences, InterPro, Protein Structure, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Web server, 570 Life Sciences, PROSITE, Biology, computer.software_genre, 01 natural sciences, Repetitive Sequences, 610 Medical Sciences, Medicine, Databases, User-Computer Interface, 03 medical and health sciences, TIGRFAMs, Computer Graphics, Genetics, Animals, Protein Databases, ddc:576, Tertiary Protein Structure, Databases, Protein, Protein Processing, 030304 developmental biology, 0303 health sciences, Database, Protein, Post-Translational, Proteins, Articles, Protein Structure, Tertiary, Amino Acid, Post translational, Cardiovascular and Metabolic Diseases, Amino Acid Repetitive Sequences, Protein processing, Protein signature, Protein Processing, Post-Translational, computer, Tertiary, Post-Translational Protein Processing, Autre (Sciences du Vivant), 010606 plant biology & botany
Abstract

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manually integrated and curated and are available in InterPro for text- and sequence-based searching. The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually. The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications. Currently, the combined signatures in InterPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since the inception of InterPro. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). more...

Published
2003
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5. Interactive InterPro-based comparisons of proteins in whole genomes

Author

Evgeni M. Zdobnov, Paul J. Kersey, Tom Oinn, Virginie Mittard, Rolf Apweiler, Evgenia V. Kriventseva, Isabelle Phan, Youla Karavidopoulou, Nicola Mulder, Wolfgang Fleischmann, Margaret Biswas, Florence Servant, and Alexander Kanapin more...

Subjects
Statistics and Probability, Protein coding, InterPro, Genome, Proteome, Computational Biology, Computational biology, Biology, computer.software_genre, Biochemistry, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, natural sciences, Data mining, Databases, Protein, Molecular Biology, computer, Software
Abstract

Motivation: The SWISS-PROT group at the EBI has developed the Proteome Analysis Database utilizing existing resources and providing comprehensive and integrated comparative analysis of the predicted protein coding sequencesof the complete genomes of bacteria, archaea and eukaryotes. The Proteome Analysis Database is accompanied by a program that has been designed to carry out interactive InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database. Availability: http://www.ebi.ac.uk/proteome/comparisons.html Contact: alex@ebi.ac.uk; proteome@ebi.ac.uk * To whom all correspondence should be addressed. more...

Published
2002
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