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2. deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets.

Author

Landerer, Cedric, Scheremetjew, Maxim, Moon, HongKee, Hersemann, Lena, and Toth-Petroczy, Agnes

Subjects
*RNA sequencing, *GENETIC transcription, *GENETIC translation, *MASS spectrometry, *GENETIC mutation
Abstract

Motivation Errors in the processing of genetic information during protein synthesis can lead to phenotypic mutations, such as amino acid substitutions, e.g. by transcription or translation errors. While genetic mutations can be readily identified using DNA sequencing, and mutations due to transcription errors by RNA sequencing, translation errors can only be identified proteome-wide using mass spectrometry. Results Here, we provide a Python package implementation of a high-throughput pipeline to detect amino acid substitutions in mass spectrometry datasets. Our tools enable users to process hundreds of mass spectrometry datasets in batch mode to detect amino acid substitutions and calculate codon-specific and site-specific translation error rates. deTELpy will facilitate the systematic understanding of amino acid misincorporation rates (translation error rates), and the inference of error models across organisms and under stress conditions, such as drug treatment or disease conditions. Availability and implementation deTELpy is implemented in Python 3 and is freely available with detailed documentation and practical examples at https://git.mpi-cbg.de/tothpetroczylab/detelpy and https://pypi.org/project/deTELpy/ and can be easily installed via pip install deTELpy. [ABSTRACT FROM AUTHOR]

Published
2024
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3. The InterPro protein families database: the classification resource after 15 years

Author

Mitchell, Alex, Chang, Hsin-Yu, Daugherty, Louise, Fraser, Matthew, Hunter, Sarah, Lopez, Rodrigo, McAnulla, Craig, McMenamin, Conor, Nuka, Gift, Pesseat, Sebastien, Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Rato, Claudia, Yong, Siew-Yit, Bateman, Alex, Punta, Marco, Attwood, Teresa K., Sigrist, Christian J.A., Redaschi, Nicole, Rivoire, Catherine, Xenarios, Ioannis, Kahn, Daniel, Guyot, Dominique, Bork, Peer, Letunic, Ivica, Gough, Julian, Oates, Matt, Haft, Daniel, Huang, Hongzhan, Natale, Darren A., Wu, Cathy H., Orengo, Christine, Sillitoe, Ian, Mi, Huaiyu, Thomas, Paul D., and Finn, Robert D.

Published
2015
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4. InterProScan 5: genome-scale protein function classification

Author

Jones, Philip, Binns, David, Chang, Hsin-Yu, Fraser, Matthew, Li, Weizhong, McAnulla, Craig, McWilliam, Hamish, Maslen, John, Mitchell, Alex, Nuka, Gift, Pesseat, Sebastien, Quinn, Antony F., Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Yong, Siew-Yit, Lopez, Rodrigo, and Hunter, Sarah

Published
2014
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5. EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

Author

Hunter, Sarah, Corbett, Matthew, Denise, Hubert, Fraser, Matthew, Gonzalez-Beltran, Alejandra, Hunter, Christopher, Jones, Philip, Leinonen, Rasko, McAnulla, Craig, Maguire, Eamonn, Maslen, John, Mitchell, Alex, Nuka, Gift, Oisel, Arnaud, Pesseat, Sebastien, Radhakrishnan, Rajesh, Rocca-Serra, Philippe, Scheremetjew, Maxim, Sterk, Peter, Vaughan, Daniel, Cochrane, Guy, Field, Dawn, and Sansone, Susanna-Assunta

Published
2014
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7. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit

Published
2012
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8. ELIXIR-EXCELERATE D6.3: Report describing a set of tools, pipelines and search engine for interrogation of marine metagenomic data

Author

Mitchell, Alex, Scheremetjew, Maxim, De Moro, Gianluca, Fosso, Bruno, Santamaria, Monica, Pesole, Graziano, Raj, Shriya, Bongo, Lars Ailo, Willassen, Nils Peder, and Finn, Robert D.

Subjects
Marine, data, tools, metagenomic, pipelines
Abstract

● Pipelines expanded to increase scope of analysis, tools updated and tailoring of analysis to meet the demands of the MarineMetagenomics community. ● Analysis pipelines described in the Common Workflow Language (CWL) to enable reproducibility, facilitate comparisons and enhance development agility. ● Benchmark datasets generated for evaluating amplicon analyses across a range of biomes and 6 different marine shotgun metagenomics datasets developed. ● Cloud deployment of pipelines to increase compute capacity. ● New data analysis outputs that will feed the databases developed as part of thiswork package. ● Examples generated for federating searches across resource programmaticinterfaces. ● Wide range of different training activities and material developed. ● Major interaction with Compute (WP4) and Interoperability (WP5) platforms insharing problems and driving solutions (e.g. AAI and CWL, respectively)

Published
2019
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9. MGnify: the microbiome analysis resource in 2020

Author

Mitchell, Alex L, primary, Almeida, Alexandre, additional, Beracochea, Martin, additional, Boland, Miguel, additional, Burgin, Josephine, additional, Cochrane, Guy, additional, Crusoe, Michael R, additional, Kale, Varsha, additional, Potter, Simon C, additional, Richardson, Lorna J, additional, Sakharova, Ekaterina, additional, Scheremetjew, Maxim, additional, Korobeynikov, Anton, additional, Shlemov, Alex, additional, Kunyavskaya, Olga, additional, Lapidus, Alla, additional, and Finn, Robert D, additional

Published
2019
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10. EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

Author

Mitchell, Alex L, primary, Scheremetjew, Maxim, additional, Denise, Hubert, additional, Potter, Simon, additional, Tarkowska, Aleksandra, additional, Qureshi, Matloob, additional, Salazar, Gustavo A, additional, Pesseat, Sebastien, additional, Boland, Miguel A, additional, Hunter, Fiona M I, additional, ten Hoopen, Petra, additional, Alako, Blaise, additional, Amid, Clara, additional, Wilkinson, Darren J, additional, Curtis, Thomas P, additional, Cochrane, Guy, additional, and Finn, Robert D, additional

Published
2017
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11. MGnify: the microbiome analysis resource in 2020.

Author

Mitchell, Alex L, Almeida, Alexandre, Beracochea, Martin, Boland, Miguel, Burgin, Josephine, Cochrane, Guy, Crusoe, Michael R, Kale, Varsha, Potter, Simon C, Richardson, Lorna J, Sakharova, Ekaterina, Scheremetjew, Maxim, Korobeynikov, Anton, Shlemov, Alex, Kunyavskaya, Olga, Lapidus, Alla, and Finn, Robert D

Published
2020
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12. The InterPro protein families database: the classification resource after 15 years

Author

Mitchell, Alex, Chang, Hsin-Yu, Daugherty, Louise, Fraser, Matthew, Hunter, Sarah, Lopez, Rodrigo, McAnulla, Craig, McMenamin, Conor, Nuka, Gift, Pesseat, Sebastien, Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Rato, Claudia, Yong, Siew-Yit, Bateman, Alex, Punta, Marco, Attwood, Teresa K., Sigrist, Christian J.A., Redaschi, Nicole, Rivoire, Catherine, Xenarios, Ioannis, Kahn, Daniel, Guyot, Dominique, Bork, Peer, Letunic, Ivica, Gough, Julian, Oates, Matt, Haft, Daniel, Huang, Hongzhan, Natale, Darren A., Wu, Cathy H., Orengo, Christine, Sillitoe, Ian, Mi, Huaiyu, Thomas, Paul D., Finn, Robert D., Mitchell, Alex, Chang, Hsin-Yu, Daugherty, Louise, Fraser, Matthew, Hunter, Sarah, Lopez, Rodrigo, McAnulla, Craig, McMenamin, Conor, Nuka, Gift, Pesseat, Sebastien, Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Rato, Claudia, Yong, Siew-Yit, Bateman, Alex, Punta, Marco, Attwood, Teresa K., Sigrist, Christian J.A., Redaschi, Nicole, Rivoire, Catherine, Xenarios, Ioannis, Kahn, Daniel, Guyot, Dominique, Bork, Peer, Letunic, Ivica, Gough, Julian, Oates, Matt, Haft, Daniel, Huang, Hongzhan, Natale, Darren A., Wu, Cathy H., Orengo, Christine, Sillitoe, Ian, Mi, Huaiyu, Thomas, Paul D., and Finn, Robert D.

Abstract

The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012

Published
2017

13. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, Yong, Siew-Yit, Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces

Published
2017

16. The InterPro protein families database: the classification resource after 15 years

Author

Mitchell, Alex, primary, Chang, Hsin-Yu, additional, Daugherty, Louise, additional, Fraser, Matthew, additional, Hunter, Sarah, additional, Lopez, Rodrigo, additional, McAnulla, Craig, additional, McMenamin, Conor, additional, Nuka, Gift, additional, Pesseat, Sebastien, additional, Sangrador-Vegas, Amaia, additional, Scheremetjew, Maxim, additional, Rato, Claudia, additional, Yong, Siew-Yit, additional, Bateman, Alex, additional, Punta, Marco, additional, Attwood, Teresa K., additional, Sigrist, Christian J.A., additional, Redaschi, Nicole, additional, Rivoire, Catherine, additional, Xenarios, Ioannis, additional, Kahn, Daniel, additional, Guyot, Dominique, additional, Bork, Peer, additional, Letunic, Ivica, additional, Gough, Julian, additional, Oates, Matt, additional, Haft, Daniel, additional, Huang, Hongzhan, additional, Natale, Darren A., additional, Wu, Cathy H., additional, Orengo, Christine, additional, Sillitoe, Ian, additional, Mi, Huaiyu, additional, Thomas, Paul D., additional, and Finn, Robert D., additional

Published
2014
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17. EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

Author

Hunter, Sarah, primary, Corbett, Matthew, additional, Denise, Hubert, additional, Fraser, Matthew, additional, Gonzalez-Beltran, Alejandra, additional, Hunter, Christopher, additional, Jones, Philip, additional, Leinonen, Rasko, additional, McAnulla, Craig, additional, Maguire, Eamonn, additional, Maslen, John, additional, Mitchell, Alex, additional, Nuka, Gift, additional, Oisel, Arnaud, additional, Pesseat, Sebastien, additional, Radhakrishnan, Rajesh, additional, Rocca-Serra, Philippe, additional, Scheremetjew, Maxim, additional, Sterk, Peter, additional, Vaughan, Daniel, additional, Cochrane, Guy, additional, Field, Dawn, additional, and Sansone, Susanna-Assunta, additional

Published
2013
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19. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, Yong, Siew-Yit, Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces

20. The InterPro protein families database: the classification resource after 15 years

Author

Mitchell, Alex, Chang, Hsin-Yu, Daugherty, Louise, Fraser, Matthew, Hunter, Sarah, Lopez, Rodrigo, McAnulla, Craig, McMenamin, Conor, Nuka, Gift, Pesseat, Sebastien, Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Rato, Claudia, Yong, Siew-Yit, Bateman, Alex, Punta, Marco, Attwood, Teresa K., Sigrist, Christian J.A., Redaschi, Nicole, Rivoire, Catherine, Xenarios, Ioannis, Kahn, Daniel, Guyot, Dominique, Bork, Peer, Letunic, Ivica, Gough, Julian, Oates, Matt, Haft, Daniel, Huang, Hongzhan, Natale, Darren A., Wu, Cathy H., Orengo, Christine, Sillitoe, Ian, Mi, Huaiyu, Thomas, Paul D., Finn, Robert D., Mitchell, Alex, Chang, Hsin-Yu, Daugherty, Louise, Fraser, Matthew, Hunter, Sarah, Lopez, Rodrigo, McAnulla, Craig, McMenamin, Conor, Nuka, Gift, Pesseat, Sebastien, Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Rato, Claudia, Yong, Siew-Yit, Bateman, Alex, Punta, Marco, Attwood, Teresa K., Sigrist, Christian J.A., Redaschi, Nicole, Rivoire, Catherine, Xenarios, Ioannis, Kahn, Daniel, Guyot, Dominique, Bork, Peer, Letunic, Ivica, Gough, Julian, Oates, Matt, Haft, Daniel, Huang, Hongzhan, Natale, Darren A., Wu, Cathy H., Orengo, Christine, Sillitoe, Ian, Mi, Huaiyu, Thomas, Paul D., and Finn, Robert D.

Abstract

The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012

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