The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Search and sequence analysis tools services from EMBL-EBI in 2022
Open accessAbstract
The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI’s data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.
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Citations
Cites
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227
Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850 · cited 1×
“IPD-NHKIR (23) coding and genomic sequences, as well as sequences from the AlphaFold DB (24), EMDB (25) and PDBe-KB, have also been made available for sequence similarity search in the JD tools framework and retrieval via Dbfetch.”
The Pfam protein families database in 2019
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky995 · Cited by 4,602
Buniello, A., MacArthur, J. A. L., Cerezo, M., Harris, L. W., Hayhurst, J., Malangone, C., McMahon, A., Morales, J., Mountjoy, E., Sollis, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1120 · Cited by 4,000
The InterPro protein families and domains database: 20 years on
Blum, M., Chang, H.-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa977 · Cited by 2,231
Cited by
Partners, C.-N. M. A., Bai, X., Bao, Y., Bei, S., Bu, C., Cao, R., Cao, Y., Cen, H., Chao, J., Chen, F., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1078 · Cited by 348
Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer
(2024) · doi:10.1038/s41467-024-51274-0 · Cited by 83
Chen, Z., Shiozaki, M., Haas, K. M., Skinner, W. M., Zhao, S., Guo, C., Polacco, B. J., Yu, Z., Krogan, N. J., Lishko, P. V., et al. (2023) · Cell · doi:10.1016/j.cell.2023.09.017 · Cited by 82
OPA1 helical structures give perspective to mitochondrial dysfunction
(2023) · doi:10.1038/s41586-023-06462-1 · Cited by 75
(2023) · doi:10.1038/s41467-023-40949-9 · Cited by 57
Metadata
- Authors
- Madeira, F., Pearce, M., Tivey, A. R. N., Basutkar, P., Lee, J., Edbali, O., Madhusoodanan, N., Kolesnikov, A., & Lopez, R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-04-12
- Volume
- 50
- Issue
- W1
- Pages
- W276-W279
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4223552703
- Cited by
- 2,267
- References
- 6
- FWCI
- 150.40
- Type
- journal article
- Language
- en
- Open access
- gold
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- Madeira, F., Pearce, M., Tivey, A. R. N., Basutkar, P., Lee, J., Edbali, O., Madhusoodanan, N., Kolesnikov, A., & Lopez, R. (2022). Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Research. https://doi.org/10.1093/nar/gkac240
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