Swelfe: A detector of internal repeats in sequences and structures

Bioinformatics

Volumn 24, Issue 13, 2008, Pages 1536-1537

  Abraham, Anne Laure ^a,b   Rocha, Eduardo P C ^a,b   Pothier, Joël ^a  

^a SORBONNE UNIVERSITÉ   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE DUPLICATION; INTERMETHOD COMPARISON; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SIMPLE SEQUENCE REPEAT; STATISTICAL SIGNIFICANCE; STRUCTURAL GENOMICS; STRUCTURAL PROTEOMICS; SYSTEM ANALYSIS; TANDEM REPEAT; WEB BROWSER;

EID: 46249097882     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn234     Document Type: Article

References (14)

1. Achaz,G. et al. (2007) Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics, 23, 119-121.
2. Benson,G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
3. Betancourt,M.R. and Skolnick,J. (2001) Universal similarity measure for comparing protein structures. Biopolymers, 59, 305-309.
4. Carpentier,M. et al. (2005) YAKUSA: A fast structural database scanning method. Proteins, 61, 137-151.
5. Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. Embo J., 5, 823-826.
6. Gibrat,J.R et al. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
7. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
8. Huang,X. and Miller,W. (1991) A time-efficient, linear-spaced local similarity algorithm. Adv. Appl. Math., 12, 337-357.
9. Huang,X.Q. et al. (1990) A space-efficient algorithm for local similarities. Comput. Appl. Biosci., 6, 373-381.
10. Kurtz,S. and Schleiermacher,C. (1999) REPuter: Fast computation of maximal repeats in complete genomes. Bioinformatics, 15, 426-427.
11. Marcotte,E.M. et al. (1999) A census of protein repeats. J. Mol. Biol., 293, 151-160.
12. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
13. Usha,R. and Murthy,M.R. (1986) Protein structural homology: A metric approach. Int. J. Pept. Protein Res., 28, 364-369.
14. Waterman,M.S. and Vingron,M. (1994) Rapid and accurate estimates of statistical significance for sequence data base searches. Proc. Natl Acad. Sci. USA, 91, 4625-4628.