DeltaProt: A software toolbox for comparative genomics

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Thorvaldsen, Steinar ^a   Flå, Tor ^a   Willassen, Nils P ^a  

^a UNIVERSITY OF TROMSØ   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMICS; ENVIRONMENTAL ADAPTATION; MULTIPLE ALIGNMENT; NUMERICAL PERFORMANCE; ORTHOLOGOUS SEQUENCES; STATISTICAL BIOINFORMATICS; STRUCTURAL INFORMATION; USER-FRIENDLY PLATFORMS;

ALGORITHMS; APPLICATION PROGRAMS; BIOINFORMATICS; GRAPHICAL USER INTERFACES; MATLAB; PROTEINS; STATISTICAL METHODS; VISUALIZATION;

DATA FLOW ANALYSIS;

PROTEIN;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER INTERFACE; COMPUTER PROGRAM; GENOMICS; METHODOLOGY; PROTEIN DATABASE; SEQUENCE ALIGNMENT;

DATABASES, PROTEIN; GENOMICS; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 78549288203     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-573     Document Type: Article

References (24)

1. Ussery DW, Wassenaar TM, Borini S. Computing for comparative microbial genomics. 2009, Springer.
2. Matlab. The MathWorks, Inc. Natick, MA (US)., http://www.mathworks.com
3. Altermark B, Thorvaldsen S, Moe E, Smalås AO, Willassen NP. Sequence comparison and environmental adaptation of a bacterial endonuclease. Computational Biology and Chemistry 2007, 31(3):163-172. 10.1016/j.compbiolchem.2007.03.003, 17500034.
4. Thorvaldsen S, Hjerde E, Fenton C, Willassen NP. Molecular characterization of cold adaptation based on ortholog protein sequences from Vibrionaceae species. Extremophiles 2007, 11(5):719-732. 10.1007/s00792-007-0093-y, 17576517.
5. Thorvaldsen S, Ytterstad E. Environmental adaptation of proteins: Regression models with simple physicochemical properties. Computational Biology and Chemistry 2009, 33(5):351-356. 10.1016/j.compbiolchem.2009.07.002, 19679511.
6. Siglioccolo A, Bossa F, Pascarella S. Structural adaptation of serine hydroxymethyltransferase to low temperatures. International Journal of Biological Macromolecules 2010, 46(1):37-46. 10.1016/j.ijbiomac.2009.09.009, 19815026.
7. Fraczkiewicz R, Braun W. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J Comp Chem 1998, 19(3):319-333.
8. Adamczak R, Porollo A, Meller J. Accurate Prediction of Solvent Accessi-bility Using Neural Networks Based Regression. Proteins: Structure, Function and Bioinformatics 2004, 56:753-767.
9. Adamczak R, Porollo A, Meller J. Combining Prediction of Secondary Structure and Solvent Accessibility in Proteins. Proteins: Structure, Function and Bioinformatics 2005, 59:467-75.
10. Gromiha MM, Oobatake M, Sarai A. Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophysical Chemistry 1999, 82(1):51-67. 10.1016/S0301-4622(99)00103-9, 10584295.
11. Kawashima S, Ogata H, Kanehisa M. AAindex: Amino Acid Index Database. Nucleic Acids Research 1999, 27(1):368-369. 10.1093/nar/27.1.368, 148186, 9847231.
12. Kendall MG, Gibbons JD. Rank Correlation Methods. 1990, Edward Arnold, 5.
13. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 1992, 8(3):275-282.
14. Chakravarty S, Varadarajan R. Elucidation of factors responsible for enhanced thermal stability of proteins: A structural genomics based study. Biochemistry 2002, 41(25):8152-8161. 10.1021/bi025523t, 12069608.
15. Agresti A. Exact inference for categorical data: recent advances and continuing controversies. Statistics in Medicine 2001, 20(17-18):2709-2722. 10.1002/sim.738, 11523078.
16. Andres AM, Quevedo MJS, Mato AS. Fisher's mid-p-value arrangement in 2×2 comparative trials. Computational Statistics & Data Analysis 1998, 29(1):107-115.
17. Agresti A. Categorical Data Analysis. 2002, John Wiley & Sons, 2.
18. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat 2001, 29(4):1165-1188.
19. Florquin K, Saeys Y, Degroeve S, Rouze P, Van de Peer Y. Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Research 2005, 33(13):4255-4264. 10.1093/nar/gki737, 1181242, 16049029.
20. Friedel M, Nikolajewa S, Suhnel J, Wilhelm T. DiProDB: a database for dinucleotide properties. Nucleic Acids Research 2009, 37(Sp Iss):D37-D40. 10.1093/nar/gkn597, 2686603, 18805906.
21. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator. Genome Research 2004, 14:1188-1190. 10.1101/gr.849004, 419797, 15173120.
22. Li W, Yang B, Liang S, Wang Y, Whiteley C, Cao Y, Wang X. BLogo: A tool for visualization of bias in biological sequences. Bioinformatics 2008, 24(19):2254-2255. 10.1093/bioinformatics/btn407, 18682425.
23. Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics 2005, 6:64. 10.1186/1471-2105-6-64, 1274259, 15780146.
24. Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution. Evolutionary Bioinformatics 2006, 2:179-182.