InterPro in 2022

Autor: Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A Salazar, Maxwell L Bileschi, Peer Bork, Alan Bridge, Lucy Colwell, Julian Gough, Daniel H Haft, Ivica Letunić, Aron Marchler-Bauer, Huaiyu Mi, Darren A Natale, Christine A Orengo, Arun P Pandurangan, Catherine Rivoire, Christian J A Sigrist, Ian Sillitoe, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Alex Bateman

Publikováno v: Nucleic Acids Research. 51:D418-D427

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (v

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::153bbcbf1ab56d7f060b0d1aec9c1f19
https://doi.org/10.1093/nar/gkac993

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

Autor: Farideh Chitsaz, Narmada Thanki, A Scott Durkin, Azat Badretdin, Jiyao Wang, Wenjun Li, Marc Gwadz, James S. Song, George Coulouris, Françoise Thibaud-Nissen, Kathleen R O’Neill, Michael DiCuccio, Aron Marchler-Bauer, Christopher J. Lanczycki, Noreen R. Gonzales, Mingzhang Yang, Chanjuan Zheng, Vyacheslav Chetvernin, Daniel H. Haft, Myra K. Derbyshire, Roxanne A. Yamashita

Publikováno v: Nucleic Acids Res

The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Genome Annotati

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f4abe9be36ae164020859ea6292a580f
https://doi.org/10.1093/nar/gkaa1105

RefSeq: an update on prokaryotic genome annotation and curation

Autor: Chanjuan Zheng, Kathleen O'Neill, Gabriele H. Marchler, Vyacheslav Chetvernin, Kim D. Pruitt, Vyacheslav Brover, Farideh Chitsaz, Françoise Thibaud-Nissen, Lewis Y. Geer, Daniel H. Haft, Michael DiCuccio, Myra K. Derbyshire, Fu Lu, Roxanne A. Yamashita, Noreen R. Gonzales, James S. Song, Aron Marchler-Bauer, Wenjun Li, Marc Gwadz, Narmada Thanki, Azat Badretdin

Publikováno v: Nucleic Acids Research

The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) provides annotation for over 95 000 prokaryotic genomes that meet standards for sequence quality, completeness, and freedom from contamination. Genome

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eb77170e990ef1713611990acbf3ae1c
https://doi.org/10.1093/nar/gkx1068

PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database

Autor: Noreen R. Gonzales, Roxanne A. Yamashita, W. John Wilbur, Aron Marchler-Bauer, Narmada Thanki, Natalie Xie, Chanjuan Zheng, Zhiyong Lu, Rezarta Islamaj

Publikováno v: Database. 2019

This study proposes a text similarity model to help biocuration efforts of the Conserved Domain Database (CDD). CDD is a curated resource that catalogs annotated multiple sequence alignment models for ancient domains and full-length proteins. These m

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::48faa0dd20a9413a5845a1cdbfadee06
https://doi.org/10.1093/database/baz064

InterPro in 2017-beyond protein family and domain annotations

Autor: Ian Sillitoe, Hsin-Yu Chang, Sara El-Gebali, Siew Yit Young, Youngmi Park, Jaina Mistry, Sebastien Pesseat, Narmada Thanki, Cathy H. Wu, Alan Bridge, Ioannis Xenarios, Ben Smithers, Simon C. Potter, Silvano Squizzato, Nicole Redaschi, Darren A. Natale, Paul Thomas, David R. Haft, Ivica Letunic, Granger G. Sutton, Silvio C. E. Tosatto, Gift Nuka, Gemma L. Holliday, Alex L. Mitchell, Teresa K. Attwood, Marco Necci, Neil D. Rawlings, Shennan Lu, Julian Gough, Alex Bateman, Patricia C. Babbitt, Lorna Richardson, Lai-Su L. Yeh, Amaia Sangrador-Vegas, Zsuzsanna Dosztányi, Rodrigo Lopez, Damiano Piovesan, Matthew Fraser, Aron Marchler-Bauer, Robert D. Finn, Peer Bork, Christine A. Orengo, Xiaosong Huang, Huaiyu Mi, Hongzhan Huang, Christian J. A. Sigrist, Catherine Rivoire

Publikováno v: Nucleic acids research, vol 45, iss D1
Finn, R D, Attwood, T K, Babbitt, P C, Bateman, A, Bork, P, Bridge, A J, Chang, H Y, Dosztanyi, Z, El-Gebali, S, Fraser, M, Gough, J, Haft, D, Holliday, G L, Huang, H, Huang, X, Letunic, I, Lopez, R, Lu, S, Marchler-Bauer, A, Mi, H, Mistry, J, Natale, D A, Necci, M, Nuka, G, Orengo, C A, Park, Y, Pesseat, S, Piovesan, D, Potter, S C, Rawlings, N D, Redaschi, N, Richardson, L, Rivoire, C, Sangrador-Vegas, A, Sigrist, C, Sillitoe, I, Smithers, B, Squizzato, S, Sutton, G, Thanki, N, Thomas, P D, Tosatto, S C E, Wu, C H, Xenarios, I, Yeh, L S, Young, S Y & Mitchell, A L 2016, ' InterPro in 2017-beyond protein family and domain annotations ', Nucleic Acids Research, vol. 45, no. D1, pp. D190-D199 . https://doi.org/10.1093/nar/gkw1107
Finn, R D, Attwood, T K, Babbitt, P C, Bateman, A, Bork, P, Bridge, A J, Chang, H-Y, Dosztányi, Z, El-Gebali, S, Fraser, M, Gough, J, Haft, D, Holliday, G L, Huang, H, Huang, X, Letunic, I, Lopez, R, Lu, S, Marchler-Bauer, A, Mi, H, Mistry, J, Natale, D A, Necci, M, Nuka, G, Orengo, C A, Park, Y, Pesseat, S, Piovesan, D, Potter, S C, Rawlings, N D, Redaschi, N, Richardson, L, Rivoire, C, Sangrador-Vegas, A, Sigrist, C, Sillitoe, I, Smithers, B, Squizzato, S, Sutton, G, Thanki, N, Thomas, P D, Tosatto, S C E, Wu, C H, Xenarios, I, Yeh, L-S, Young, S-Y & Mitchell, A L 2017, ' InterPro in 2017-beyond protein family and domain annotations ', Nucleic acids research, vol. 45, no. D1, pp. D190-D199 . https://doi.org/10.1093/nar/gkw1107
Nucleic Acids Research

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::09ef53ce889ada380b316e2da5a8c210
http://hdl.handle.net/11577/3230382