The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Protein sequence similarity searches using patterns as seeds
Open accessAbstract
Protein families often are characterized by conserved sequence patterns or motifs. A researcher frequently wishes to evaluate the significance of a specific pattern within a protein, or to exploit knowledge of known motifs to aid the recognition of greatly diverged but homologous family members. To assist in these efforts, the pattern-hit initiated BLAST (PHI-BLAST) program described here takes as input both a protein sequence and a pattern of interest that it contains. PHI-BLAST searches a protein database for other instances of the input pattern, and uses those found as seeds for the construction of local alignments to the query sequence. The random distribution of PHI-BLAST alignment scores is studied analytically and empirically. In many instances, the program is able to detect statistically significant similarity between homologous proteins that are not recognizably related using traditional single-pass database search methods. PHI-BLAST is applied to the analysis of CED4-like cell death regulators, HS90-type ATPase domains, archaeal tRNA nucleotidyltransferases and archaeal homologs of DnaG-type DNA primases.
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Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Cited by
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
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1195 · Cited by 3,261
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Ostell, J., Pruitt, K. D., & Sayers, E. W. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1094 · Cited by 760
CAMP R3 : a database on sequences, structures and signatures of antimicrobial peptides: Table 1.
Waghu, F. H., Barai, R. S., Gurung, P., & Idicula-Thomas, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1051 · Cited by 715
Lechner, M. S., Begg, G. E., Speicher, D. W., & Rauscher, F. J. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.17.6449-6465.2000 · Cited by 210
Metadata
- Authors
- Zhang, Z.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1998-09-01
- Volume
- 26
- Issue
- 17
- Pages
- 3986-3990
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1995260859
- Cited by
- 342
- References
- 1
- FWCI
- 7.09
- Type
- journal article
- Language
- en
- Open access
- bronze
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