A census of protein repeats

Journal of Molecular Biology

Volumn 293, Issue 1, 1999, Pages 151-160

  Marcotte, Edward M ^a   Pellegrini, Matteo ^a   Yeates, Todd O ^a   Eisenberg, David ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Duplication; Genomic analysis; Microsatellite; Minisatellite; Protein evolution

Indexed keywords

REPETITIVE DNA;

AMINO ACID SEQUENCE; ARTICLE; EUKARYOTE; GENOME; INCIDENCE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROKARYOTE;

EUKARYOTA; PROKARYOTA;

EID: 0033569354     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3136     Document Type: Article

References (29)

1. Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucl. Acids Res. 27:1998;49-54.
2. Bateman A., Birney E., Durbin R., Eddy S. R., Finn R. D., Sonnhammer E. L. Pfam 3.1: 1313 multiple alignments match the majority of proteins. Nucl. Acids Res. 27:1999;260-262.
3. Brenner S. E., Hubbard T., Murzin A., Chothia C. Gene duplications in H. influenzae. Nature. 378:1995;140.
4. Buard J., Vergnaud G. Complex recombination events at the hypermutable minisatellite CEB1 (D2S90). EMBO J. 13:1997;3203-3210.
5. Conti E., Uy M., Leighton L., Blobel G., Kuriyan J. Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Cell. 94:1998;193-204.
6. Djian P. Evolution of simple repeats in DNA and their relation to human diseases. Cell. 94:1998;155-160.
7. Fauchere J., Pliska V. Hydrophobic parameters π of amino acid side-chains from the partitioning of N -acetyl-amino-acid amides. Eur. J. Med. Chem. 18:1983;369-375.
8. Fitz-Gibbon S. T. Whole genome sequence of the hyperthermophilic archaeon Pyrobaculum aerophilum, PhD dissertation. 1998;University of California, Los Angeles.
9. Fossella J. A., Kim Y. J., Shih H., Richards E. G., Fresco J. R. Relative specificities in binding of Watson-Crick base-pairs by third strand residues in a DNA pyrimidine triplex motif. Nucl. Acids Res. 21:1993;4511-4515.
10. Gerstein M. A structural census of genomes: comparing bacterial, eukaryotic, and archael genomes in terms of protein structure. J. Mol. Biol. 274:1997;562-576.
11. Heringa J. Detection of internal repeats: how common are they? Curr. Opin. Struct. Biol. 8:1998;338-345.
12. Heringa J., Argos P. A method to recognize distant repeats in protein sequences. Proteins: Struct. Funct. Genet. 17:1993;391-411.
13. Hofmann K., Bucher P., Falquet L., Bairoch A. The PROSITE database, its status in 1999. Nucl. Acids Res. 27:1999;215-219.
14. Kachroo P., Ahuja M., Leong S. A., Chattoo B. B. Organisation and molecular analysis of repeated DNA sequences in the rice blast fungus Magnaporthe grisea. Curr. Genet. 31:1997;361-369.
15. Kobe B., Deisenhofer J. Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. Nature. 366:1993;751-756.
16. Koonin E. V., Mushegian A. R., Galperin M. Y., Walker D. R. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25:1997;619-637.
17. Kruglyak S., Durrett R. T., Schug M. D., Aquadro C. F. Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc. Natl Acad. Sci. USA. 95:1998;10774-10778.
18. Leeflang E. P., Zhang L., Tavare S., Hubert R., Srinidhi J., MacDonald M. E., Myers R. H., de Young M., Wexler N. S., Arnheim N., Gusella J. F. Single sperm analysis of the trinucleotide repeats in the Huntington's disease gene: quantification of the mutation frequency spectrum. Human. Mol. Genet. 4:1995;1519-1526.
19. McLachlan A. D. Analysis of gene duplication repeats in the myosin rods. J. Mol. Biol. 169:1983;15-30.
20. Moxon E. R., Rainey P. B., Nowak M. A., Lenski R. E. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4:1994;24-33.
21. Netzer W. J., Hartl F. U. Recombination of protein domains facilitated by co-translational folding in eukaryotes. Nature. 388:1997;343-349.
22. Pellegrini M., Marcotte E. M., Yeates T. O. A fast algorithm for genome-wide analysis of proteins with repeated sequences. Proteins: Struct. Funct. Genet. 35:1999;440-446.
23. Radzicka A., Wolfenden R. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry. 27:1988;1664-1670.
24. Reiss A. L., Kazazian H. H. Jr, Krebs C. M., McAughan A., Boehm C. D., Abrams M. T., Nelson D. L. Frequency and stability of the fragile X premutation. Human Mol. Genet. 3:1994;393-398.
25. Smith T. F., Waterman M. S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197.
26. Tomb J. F., White O., Kerlavage A. R., Clayton R. A., Sutton G. G., Fleischmann R. D., Ketchum K. A., Klenk H. P., Gill S., Dougherty B. A., Nelson K., Quackenbush J., Zhou L., Kirkness E. F., Peterson S. et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 388:1997;539-547.
27. Waterman M. S., Eggert M. A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol. 197:1987;723-728.
28. Waterman M. S., Vingron M. Sequence comparison significance and Poisson approximation. Stat. Sci. 9:1994;367-381.
29. Wootton J. C., Federhen S. Statistics of local complexity in amino acid sequences and sequence databases. Comp. Chem. 17:1993;149-163.