Nucleic Acids Research, Vol 26, Issue 17 3986-3990, Copyright © 1998 by Oxford University Press
Z Zhang, AA Schaffer, W Miller, TL Madden, DJ Lipman, EV Koonin and SF Altschul
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.
ARTICLES
Protein sequence similarity searches using patterns as seeds
Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. M. Gould, F. Diella, A. Via, P. Puntervoll, C. Gemund, S. Chabanis-Davidson, S. Michael, A. Sayadi, J. C. Bryne, C. Chica, et al. ELM: the status of the 2010 eukaryotic linear motif resource Nucleic Acids Res., November 17, 2009; (2009) gkp1016v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and E. W. Sayers GenBank Nucleic Acids Res., November 12, 2009; (2009) gkp1024v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Joseph and D. Durand Family classification without domain chaining Bioinformatics, June 15, 2009; 25(12): i45 - i53. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Braasch, J.-N. Volff, and M. Schartl The Endothelin System: Evolution of Vertebrate-Specific Ligand-Receptor Interactions by Three Rounds of Genome Duplication Mol. Biol. Evol., April 1, 2009; 26(4): 783 - 799. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and E. W. Sayers GenBank Nucleic Acids Res., January 1, 2009; 37(suppl_1): D26 - D31. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Andreeva and H. Tidow A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes Bioinformatics, October 15, 2008; 24(20): 2277 - 2280. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. E. Ortiz-Soto, M. Rivera, E. Rudino-Pinera, C. Olvera, and A. Lopez-Munguia Selected mutations in Bacillus subtilis levansucrase semi-conserved regions affecting its biochemical properties Protein Eng. Des. Sel., October 1, 2008; 21(10): 589 - 595. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Shu, T. Zhou, and S. Hovmoller Prediction of zinc-binding sites in proteins from sequence Bioinformatics, March 15, 2008; 24(6): 775 - 782. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler GenBank Nucleic Acids Res., January 11, 2008; 36(suppl_1): D25 - D30. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Heger, S. Mallick, C. Wilton, and L. Holm The global trace graph, a novel paradigm for searching protein sequence databases Bioinformatics, September 15, 2007; 23(18): 2361 - 2367. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. W. Brown, R. A. E. Butchko, M. Busman, and R. H. Proctor The Fusarium verticillioides FUM Gene Cluster Encodes a Zn(II)2Cys6 Protein That Affects FUM Gene Expression and Fumonisin Production Eukaryot. Cell, July 1, 2007; 6(7): 1210 - 1218. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Papadopoulos and R. Agarwala COBALT: constraint-based alignment tool for multiple protein sequences Bioinformatics, May 1, 2007; 23(9): 1073 - 1079. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler GenBank Nucleic Acids Res., January 12, 2007; 35(suppl_1): D21 - D25. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Hao, J. Klein, and M. Nei Heterogeneous but conserved natural killer receptor gene complexes in four major orders of mammals PNAS, February 28, 2006; 103(9): 3192 - 3197. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. B. Thomas and R. I. Gumport Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase Nucleic Acids Res., February 6, 2006; 34(3): 806 - 815. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler GenBank Nucleic Acids Res., January 1, 2006; 34(suppl_1): D16 - D20. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Pugalenthi, A. Bhaduri, and R. Sowdhamini iMOTdb--a comprehensive collection of spatially interacting motifs in proteins Nucleic Acids Res., January 1, 2006; 34(suppl_1): D285 - D286. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Bickel, L. Lehle, M. Schwarz, M. Aebi, and C. A. Jakob Biosynthesis of Lipid-linked Oligosaccharides in Saccharomyces cerevisiae: Alg13p AND Alg14p FORM A COMPLEX REQUIRED FOR THE FORMATION OF GlcNAc2-PP-DOLICHOL J. Biol. Chem., October 14, 2005; 280(41): 34500 - 34506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Chakrabarti, A. P. Anand, N. Bhardwaj, G. Pugalenthi, and R. Sowdhamini SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs Nucleic Acids Res., July 1, 2005; 33(suppl_2): W274 - W276. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. G. Bowden, W. Chen, J. Singvall, Y. Xu, S. J. Peacock, V. Valtulina, P. Speziale, and M. Hook Identification and preliminary characterization of cell-wall-anchored proteins of Staphylococcus epidermidis Microbiology, May 1, 2005; 151(5): 1453 - 1464. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. G. Conticello, C. J. F. Thomas, S. K. Petersen-Mahrt, and M. S. Neuberger Evolution of the AID/APOBEC Family of Polynucleotide (Deoxy)cytidine Deaminases Mol. Biol. Evol., February 1, 2005; 22(2): 367 - 377. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler GenBank Nucleic Acids Res., January 1, 2005; 33(suppl_1): D34 - D38. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Pugalenthi, A. Bhaduri, and R. Sowdhamini GenDiS: Genomic Distribution of protein structural domain Superfamilies Nucleic Acids Res., January 1, 2005; 33(suppl_1): D252 - D255. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. B. Lobocka, D. J. Rose, G. Plunkett III, M. Rusin, A. Samojedny, H. Lehnherr, M. B. Yarmolinsky, and F. R. Blattner Genome of Bacteriophage P1 J. Bacteriol., November 1, 2004; 186(21): 7032 - 7068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Alam, A. Dress, M. Rehmsmeier, and G. Fuellen Comparative homology agreement search: An effective combination of homology-search methods PNAS, September 21, 2004; 101(38): 13814 - 13819. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. McGinnis and T. L. Madden BLAST: at the core of a powerful and diverse set of sequence analysis tools Nucleic Acids Res., July 1, 2004; 32(suppl_2): W20 - W25. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Q.-l. Wang, S. Chen, N. Esumi, P. K. Swain, H. S. Haines, G. Peng, B. M. Melia, I. McIntosh, J. R. Heckenlively, S. G. Jacobson, et al. QRX, a novel homeobox gene, modulates photoreceptor gene expression Hum. Mol. Genet., May 15, 2004; 13(10): 1025 - 1040. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler GenBank: update Nucleic Acids Res., January 1, 2004; 32(90001): D23 - 26. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bhaduri and R. Sowdhamini A genome-wide survey of human tyrosine phosphatases Protein Eng. Des. Sel., December 1, 2003; 16(12): 881 - 888. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Papazisi, T. S. Gorton, G. Kutish, P. F. Markham, G. F. Browning, D. K. Nguyen, S. Swartzell, A. Madan, G. Mahairas, and S. J. Geary The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain Rlow Microbiology, September 1, 2003; 149(9): 2307 - 2316. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. M. McGinnis, S. G. Thomas, J. D. Soule, L. C. Strader, J. M. Zale, T.-p. Sun, and C. M. Steber The Arabidopsis SLEEPY1 Gene Encodes a Putative F-Box Subunit of an SCF E3 Ubiquitin Ligase PLANT CELL, May 1, 2003; 15(5): 1120 - 1130. [Abstract] [Full Text]
|
|
|
|
|
|
G. K-W. Kong, G. Polekhina, W. J. McKinstry, M. W. Parker, B. Dragani, A. Aceto, D. Paludi, D. R. Principe, B. Mannervik, and G. Stenberg Contribution of Glycine 146 to a Conserved Folding Module Affecting Stability and Refolding of Human Glutathione Transferase P1-1 J. Biol. Chem., January 3, 2003; 278(2): 1291 - 1302. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler GenBank Nucleic Acids Res., January 1, 2003; 31(1): 23 - 27. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. van der Wel, H. R. Morris, M. Panico, T. Paxton, A. Dell, L. Kaplan, and C. M. West Molecular Cloning and Expression of a UDP-N-acetylglucosamine (GlcNAc):Hydroxyproline Polypeptide GlcNAc-transferase That Modifies Skp1 in the Cytoplasm of Dictyostelium J. Biol. Chem., November 22, 2002; 277(48): 46328 - 46337. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-H. Feng, Y. Sun, and J. G. Douglas Gbeta gamma -independent constitutive association of Galpha s with SHP-1 and angiotensin II receptor AT2 is essential in AT2-mediated ITIM-independent activation of SHP-1 PNAS, September 17, 2002; 99(19): 12049 - 12054. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-S. Lee, M.-S. Kim, H.-S. Cho, J.-I. Kim, T.-J. Kim, J.-H. Choi, C. Park, H.-S. Lee, B.-H. Oh, and K.-H. Park Cyclomaltodextrinase, Neopullulanase, and Maltogenic Amylase Are Nearly Indistinguishable from Each Other J. Biol. Chem., June 7, 2002; 277(24): 21891 - 21897. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp, and D. L. Wheeler GenBank Nucleic Acids Res., January 1, 2002; 30(1): 17 - 20. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Tatsuno, M. Horie, H. Abe, T. Miki, K. Makino, H. Shinagawa, H. Taguchi, S. Kamiya, T. Hayashi, and C. Sasakawa toxB Gene on pO157 of Enterohemorrhagic Escherichiacoli O157:H7 Is Required for Full Epithelial Cell Adherence Phenotype Infect. Immun., November 1, 2001; 69(11): 6660 - 6669. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. J. Turano, G. R. Panta, M. W. Allard, and P. van Berkum The Putative Glutamate Receptors from Plants Are Related to Two Superfamilies of Animal Neurotransmitter Receptors via Distinct Evolutionary Mechanisms Mol. Biol. Evol., July 1, 2001; 18(7): 1417 - 1420. [Full Text] [PDF]
|
|
|
|
|
|
D. L. Wheeler, D. M. Church, A. E. Lash, D. D. Leipe, T. L. Madden, J. U. Pontius, G. D. Schuler, L. M. Schriml, T. A. Tatusova, L. Wagner, et al. Database resources of the National Center for Biotechnology Information Nucleic Acids Res., January 1, 2001; 29(1): 11 - 16. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Aravind, K. S. Makarova, and E. V. Koonin SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories Nucleic Acids Res., September 15, 2000; 28(18): 3417 - 3432. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. S. Lechner, G. E. Begg, D. W. Speicher, and F. J. Rauscher III Molecular Determinants for Targeting Heterochromatin Protein 1-Mediated Gene Silencing: Direct Chromoshadow Domain-KAP-1 Corepressor Interaction Is Essential Mol. Cell. Biol., September 1, 2000; 20(17): 6449 - 6465. [Abstract] [Full Text]
|
|
|
|
|
|
Q. Lu and E. Henderson Two Tetrahymena G-DNA-binding proteins, TGP1 and TGP3, share novel motifs and may play a role in micronuclear division Nucleic Acids Res., August 1, 2000; 28(15): 2993 - 3001. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z.-s. Zhao, E. Manser, and L. Lim Interaction between PAK and Nck: a Template for Nck Targets and Role of PAK Autophosphorylation Mol. Cell. Biol., June 1, 2000; 20(11): 3906 - 3917. [Abstract] [Full Text]
|
|
|
|
|
|
D. Solecki, G. Bernhardt, M. Lipp, and E. Wimmer Identification of a Nuclear Respiratory Factor-1 Binding Site within the Core Promoter of the human polio virus receptor/CD155 Gene J. Biol. Chem., April 21, 2000; 275(17): 12453 - 12462. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-J. Bey, M.-F. Tsou, C.-H. Huang, C.-C. Yang, and C. W. Chen The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid Microbiology, April 1, 2000; 146(4): 911 - 922. [Abstract] [Full Text]
|
|
|
|
|
|
L. Essers, R. H. Adolphs, and R. Kunze A Highly Conserved Domain of the Maize Activator Transposase Is Involved in Dimerization PLANT CELL, February 1, 2000; 12(2): 211 - 224. [Abstract] [Full Text]
|
|
|
|
|
|
D. L. Wheeler, C. Chappey, A. E. Lash, D. D. Leipe, T. L. Madden, G. D. Schuler, T. A. Tatusova, and B. A. Rapp Database resources of the National Center for Biotechnology Information Nucleic Acids Res., January 1, 2000; 28(1): 10 - 14. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp, and D. L. Wheeler GenBank Nucleic Acids Res., January 1, 2000; 28(1): 15 - 18. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Rosati, S. Pozzi, P. Robino, B. Montinaro, A. Conti, M. Fadda, and M. Pittau P48 Major Surface Antigen of Mycoplasma agalactiae Is Homologous to a malp Product of Mycoplasma fermentans and Belongs to a Selected Family of Bacterial Lipoproteins Infect. Immun., November 1, 1999; 67(11): 6213 - 6216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Rosenblum and G. Blobel Autoproteolysis in nucleoporin biogenesis PNAS, September 28, 1999; 96(20): 11370 - 11375. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. V. Venkatachalam, H. Fuda, E. V. Koonin, and C. A. Strott Site-selected Mutagenesis of a Conserved Nucleotide Binding HXGH Motif Located in the ATP Sulfurylase Domain of Human Bifunctional 3'-Phosphoadenosine 5'-Phosphosulfate Synthase J. Biol. Chem., January 29, 1999; 274(5): 2601 - 2604. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Nadimpalli, N. Yalpani, G. S. Johal, and C. R. Simmons Prohibitins, Stomatins, and Plant Disease Response Genes Compose a Protein Superfamily That Controls Cell Proliferation, Ion Channel Regulation, and Death J. Biol. Chem., September 15, 2000; 275(38): 29579 - 29586. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Kanaya, K. Watanabe, N. Nakajima, K. Okada, and Y. Shimura Zinc Release from the CH2C6 Zinc Finger Domain of FILAMENTOUS FLOWER Protein from Arabidopsis thaliana Induces Self-assembly J. Biol. Chem., March 2, 2001; 276(10): 7383 - 7390. [Abstract] [Full Text] [PDF]
|
|