Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Hu, Jing ^a   Yan, Changhui ^a  

^a Utah State University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED METHODS; CORRELATION COEFFICIENT; DECISION TREE METHOD; GREEDY APPROACHES; OVERALL ACCURACIES; PROTEIN SEQUENCES; PROTEIN STRUCTURES; SINGLE NUCLEOTIDE POLYMORPHISMS;

AMINO ACIDS; FORESTRY; NUCLEOTIDES; PROTEINS;

INFORMATION USE;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; COMPUTER PREDICTION; CONTROLLED STUDY; CORRELATION COEFFICIENT; DECISION TREE; FEASIBILITY STUDY; GENE MUTATION; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MOLECULAR SYSTEMATICS; PROTEIN DATABASE; RESIDUE ANALYSIS; SENSITIVITY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; BIOLOGY; DNA SEQUENCE; HUMAN; METHODOLOGY; SEQUENCE ANALYSIS;

ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN;

EID: 47149104909     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-297     Document Type: Article

References (32)

1. Collins FS Brooks LD Chakravarti A A DNA Polymorphism Discovery Resource for Research on Human Genetic Variation Genome Res 1998, 8:1229-1231
2. Stenson PD Ball EV Mort M Phillips AD Shiel JA Thomas NST Abeysinghe S Krawczak M Cooper DN Human Gene Mutation Database (HGMD): 2003 update Human Mutation 2003, 21:577-581 10.1002/humu.10212
3. Ng PC Henikoff S Accounting for Human Polymorphisms Predicted to Affect Protein Function Genome Res 2002, 12:436-446 10.1101/gr.212802
4. Bell J Predicting disease using genomics Nature 2004, 429:453-456 10.1038/nature02624
5. Sherry ST Ward MH Kholodov M Baker J Phan L Smigielski EM Sirotkin K dbSNP: The NCBI database of genetic variation Nucl Acids Res 2001, 29:308-311 10.1093/nar/29.1.308
6. Fredman D Munns G Rios D Sjoholm F Siegfried M Lenhard B Lehvaslaiho H Brookes AJ HGVbase: A curated resource describing human DNA variation and phenotype relationships Nucl Acids Res 2004, 32:D516-519 10.1093/nar/ gkh111
7. Yip YL Scheib H Diemand AV Gattiker A Famiglietti LM Gasteiger E Bairoch A The Swiss-Prot variant page and the ModSNP database: A resource for sequence and structure information on human protein variants Human Mutation 2004, 23:464-470 10.1002/humu.20021
8. Herrgard S Cammer SA Hoffman BT Knutson S Gallina M Speir JA Fetrow JS Baxter SM Prediction of deleterious functional effects of amino acid mutations using a library of structure-based function descriptors Proteins: Structure, Function, and Genetics 2003, 53:806-816 10.1002/ prot.10458
9. Ng PC Henikoff S Predicting Deleterious Amino Acid Substitutions Genome Res 2001, 11:863-874 10.1101/gr.176601
10. Chasman D Adams RM Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation Journal of Molecular Biology 2001, 307:683-706 10.1006/jmbi.2001.4510
11. Dobson R Munroe P Caulfield M Saqi M Predicting deleterious nsSNPs: An analysis of sequence and structural attributes BMC Bioinformatics 2006, 7:217 10.1186/1471-2105-7-217
12. Krishnan VG Westhead DR A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function Bioinformatics 2003, 19:2199-2209 10.1093/bioinformatics/btg297
13. Bao L Cui Y Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information Bioinformatics 2005, 21:2185-2190 10.1093/bioinformatics/ bti365
14. Ferrer-Costa C Orozco M Cruz X Use of bioinformatics tools for the annotation of disease-associated mutations in animal models Proteins: Structure, Function, and Bioinformatics 2005, 61:878-887 10.1002/ prot.20664
15. Bromberg Y Rost B SNAP: Predicting effect of non-synonymous polymorphisms on function Nucl Acids Res 2007, 35:3823-3835 10.1093/nar/ gkm238
16. Capriotti E Calabrese R Casadio R Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information Bioinformatics 2006, 22:2729-2734 10.1093/bioinformatics/btl423
17. Yue P Li Z Moult J Loss of Protein Structure Stability as a Major Causative Factor in Monogenic Disease Journal of Molecular Biology 2005, 353:459-473 10.1016/j.jmb.2005.08.020
18. Ye ZQ Zhao SQ Gao G Liu XQ Langlois RE Lu H Wei L Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP) Bioinformatics 2007, 23:1444-1450 10.1093/bioinformatics/btm119
19. Kawashima S Ogata H Kanehisa M AAindex: Amino Acid Index Database Nucl Acids Res 1999, 27:368-369 10.1093/nar/27.1.368
20. Baldi P Brunak S Chauvin Y Andersen CAF Assessing the accuracy of prediction algorithms for classification: An overview Bioinformatics 2000, 16:412-424 10.1093/bioinformatics/16.5.412
21. Ng PC Henikoff S SIFT: Predicting amino acid changes that affect protein function Nucl Acids Res 2003, 31:3812-3814 10.1093/nar/gkg509
22. Mi H Guo N Kejariwal A Thomas PD PANTHER version 6: Protein sequence and function evolution data with expanded representation of biological pathways Nucl Acids Res 2007, 35:D247-252 10.1093/nar/gkl869
23. Kawabata T Ota M Nishikawa K The Protein Mutant Database Nucl Acids Res 1999, 27:355-357 10.1093/nar/27.1.355
24. SAPs from SwissProt http://gpcr2.biocomp.unibo.it/~emidio/PhD-SNP/ HumVar.txt
25. Witten IH Frank E Data Mining: Practical machine learning tools and techniques San Francisco, Morgan Kaufmann 2nd 2005
26. Online server for SAPs prediction http://yanbioinformatics.cs.usu.edu:8080/SAPsubmit
27. Dayhoff MO Schwartz RM Orcutt BC A model of evolutionary change in proteins Atlas of Protein Sequence and Structure Washington, D.C., National Biomedical Research Foundation Dayhoff MO 1978, 5:352
28. Feng DF Johnson MS Doolittle RF Aligning amino acid sequences: comparison of commonly used methods J Mol Evol 1985, 21:112-125 10.1007/ BF02100085 6100188
29. Zhang C Kim SH Environment-dependent residue contact energies for proteins Proceedings of the National Academy of Sciences 2000, 97:2550-2555 10.1073/pnas.040573597 10706611 15966
30. Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks Proc Natl Acad Sci U S A 1992, 89:10915-10919 10.1073/ pnas.89.22.10915 1438297 50453
31. Nakashima H K. N Ooi T Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins Proteins 1990, 8:173-178 10.1002/prot.340080207
32. Miyazawa S Jernigan RL Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation Macromolecules 1985, 18:534-552 10.1021/ma00145a039