ProBias: A web-server for the identification of user-specified types of compositionally biased segments in protein sequences

Bioinformatics

Volumn 24, Issue 13, 2008, Pages 1534-1535

  Kuznetsov, Igor B ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; HUMAN COMPUTER INTERACTION; INFORMATION PROCESSING; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN DOMAIN; SEARCH ENGINE; SEQUENCE ANALYSIS; STATISTICAL SIGNIFICANCE; STRUCTURAL PROTEOMICS; SYSTEM ANALYSIS; SYSTEMATIC ERROR; WEB BROWSER;

EID: 46249090789     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn233     Document Type: Article

References (18)

1. Alba,M.M. et al. (2002) Detecting cryptically simple protein sequences using the SIMPLE algorithm. Bioinformatics, 8, 672-678.
2. Brendel,V. et al. (1992) Methods and algorithms for statistical analysis of protein sequences. Proc. Natl Acad. Sci. USA, 89 2002-2006.
3. Claverie,J.-M. and States,D.J. (1993) Information enhancement methods for large scale sequence analysis. Comput. Chem., 17, 191-201.
4. DeMarco,M.L. and Daggett,V. (2007) Molecular mechanism for low pH triggered misfolding of the human prion protein. Biochemistry, 46, 3045-3054.
5. Eisenhaber,F. et al. (2003) Prediction of lipid posttranslational modifications and localization signals from protein sequences: Big-Pi, NMT and PTS1. Nucleic Acids Res., 31, 3631-3634.
6. Glaz,J. et al. (2001) Scan Statistics. Springer-Verlag, New York, pp. 45-46.
7. Gunawardena,S. and Goldstein,L.S. (2005) Polyglutamine diseases and transport problems: Deadly traffic jams on neuronal highways. Arch Neurol., 62, 46-51.
8. Harrison,P.M. (2006) Exhaustive assignment of compositional bias reveals universally prevalent biased regions: Analysis of functional associations in human and Drosophila. BMC Bioinformatics, 7, 441.
9. Harrison,P.M. and Gerstein,M. (2003) A method to assess compositional bias in biological sequences and its application to prion-like glutamine/ asparagine-rich domains in eukaryotic proteomes. Genome Biol., 4, R40.
10. Karlin,S. et al. (2003) Genome comparisons and analysis. Curr. Opin. Struct. Biol., 13, 344-352.
11. Koonin,E.V. et al. (1996) Protein sequence comparison at genome scale. Methods Enzymol., 266, 295-322.
12. Kreil,D.P. and Ouzounis,C.A. (2003) Comparison of sequence masking algorithms and the detection of biased protein sequence regions. Bioinformatics, 19, 1672-1681.
13. Kuznetsov,I.B. and Hwang,S. (2006) A novel sensitive method for the detection of user-defined compositional bias in biological sequences. Bioinformatics, 22, 1055-1063.
14. Li,X. and Kahveci,T (2006) A novel algorithm for identifying low-complexity regions in a protein sequence. Bioinformatics, 22, 2980-2987.
15. Promponas,V.J. et al. (2000) CAST: An iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics, 16, 915-922.
16. Romero,P. et al. (2004) Natively disordered proteins: Functions and predictions. Appl. Bioinformatics, 3, 105-113.
17. Shin,S.W. and Kim,S.M. (2005) A new algorithm for detecting low-complexity regions in protein sequences. Bioinformatics, 21 160-170.
18. Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.