The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
An Introduction to Sequence Similarity (“Homology”) Searching
Open accessAbstract
Sequence similarity searching, typically with BLAST, is the most widely used and most reliable strategy for characterizing newly determined sequences. Sequence similarity searches can identify “homologous” proteins or genes by detecting excess similarity— statistically significant similarity that reflects common ancestry. This unit provides an overview of the inference of homology from significant similarity, and introduces other units in this chapter that provide more details on effective strategies for identifying homologs. Curr. Protoc. Bioinform. 42:3.1.1‐3.1.8. © 2013 by John Wiley & Sons, Inc.
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Cited by
Large language models generate functional protein sequences across diverse families
Madani, A., Krause, B., Greene, E. R., Subramanian, S., Mohr, B. P., Holton, J. M., Olmos, J. L., Xiong, C., Sun, Z. Z., Socher, R., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01618-2 · Cited by 1,078
Single-sequence protein structure prediction using language models from deep learning
Chowdhury, R., Bouatta, N., Biswas, S., Rochereau, C., Church, G. M., Sorger, P. K., & AlQuraishi, M. (2021) · doi:10.1101/2021.08.02.454840 · Cited by 455
“…using ML nonetheless remains a challenge: the requirement in AlphaFold2 for co-evolutionary information from MSAs makes it less performative with proteins that lack sequence homologs, currently estimated at ~20% of all metagenomic protein sequences 9 and ~11% of eukaryotic and viral proteins 10 .”
BackgroundSingle-sequence protein structure prediction using a language model and deep learning
Chowdhury, R., Bouatta, N., Biswas, S., Floristean, C., Kharkar, A., Roy, K., Rochereau, C., Ahdritz, G., Zhang, J., Church, G. M., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01432-w · Cited by 455
Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota
Rampelli, S., Schnorr, S. L., Consolandi, C., Turroni, S., Severgnini, M., Peano, C., Brigidi, P., Crittenden, A. N., Henry, A. G., & Candela, M. (2015) · Current Biology · doi:10.1016/j.cub.2015.04.055 · Cited by 399
Porebski, B. T., & Buckle, A. M. (2016) · Protein Engineering Design and Selection · doi:10.1093/protein/gzw015 · Cited by 215
Metadata
- Authors
- Pearson, W. R.
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2013-06
- Volume
- 42
- Issue
- 1
- Pages
- 3.1.1-3.1.8
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- OpenAlex
- W2166637863
- Cited by
- 937
- References
- 1
- FWCI
- 6.72
- Type
- journal article
- Language
- en
- Open access
- green
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