Unique peptide identification of RNaseA superfamily sequences based on reinforced merging algorithms

Journal of Bioinformatics and Computational Biology

Volumn 4, Issue 1, 2006, Pages 75-92

  Pai, Tun Wen ^a   Su, Bo Han ^a   Wu, Pei Chih ^a   Chang, Margaret Dah Tsyr ^b   Chang, Hao Teng ^b   Fan, Tan Chi ^b   Liu, Shi Hwei ^b  

^a NATIONAL TAIWAN OCEAN UNIVERSITY   (Taiwan)

^b NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

Reinforced merging algorithm; Ribonuclease A superfamily; Unique peptide

Indexed keywords

AMINO ACID; DNA; EPITOPE; MONOCLONAL ANTIBODY; RIBONUCLEASE A;

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; EXPERIMENTAL DESIGN; GENETIC CONSERVATION; HUMAN; INTERNET; PANCREAS; PEPTIDE ANALYSIS; PREDICTION; PROTEIN FAMILY; PROTEIN MOTIF; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; ANTIBODIES, MONOCLONAL; ANTIBODY SPECIFICITY; CATTLE; COMPUTATIONAL BIOLOGY; EPITOPE MAPPING; HUMANS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; RIBONUCLEASE, PANCREATIC; SEQUENCE ANALYSIS, PROTEIN;

BOVINAE;

EID: 33645291467     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720006001710     Document Type: Article

References (28)

1. D'Alessio G, New and cryptic biological messages from RNases, Trends Cell Biol 3(4):106-109, 1993.
2. Weickmann JL, Elson M, Glitz DG, Purification and characterization of human pancreatic ribonuclease, Biochemistry 20(5):1272-1278, 1981.
3. Slifman NR et al., Ribonuclase activity associated with human eosinophil-derived neurotoxin and eosinophil cationic protein, J Immunol 137:2913-2917, 1986.
4. Olssom I, Venge P, Cationic proteins of human granulocytes. I. Isolation of the cationic proteins from the granules of leukaemic myeloid cells, Scand J Haematol 9:204-214, 1972.
5. Rosenberg HF, Dyer KD, Human ribonuclease 4 (RNase 4): Coding sequence, chromosomal localization and identification of two distinct transcripts in human somatic tissues, Nucleic Acids Res 23(21):4290-4295, 1995.
6. Strydom DJ et al., Amino acid sequence of human tumor derived angiogenin, Biochemistry 24(20):5486-5494, 1985.
7. Rosenberg HF, Dyer KD, Molecular cloning and characterization of a noval human ribonuclease (RNase k6): Increasing diversity in the enlarging ribonuclease gene family, Nucleic Acids Res 24:3507-3513, 1996.
8. Zhang J, Dyer KD, Rosenberg HF, Human RNase 7: A new cationic ribonuclease of the RNase A superfamily, Nucleic Acids Res 31(2):602-607, 2003.
9. Zhang J, Dyer KD, Rosenberg HF, RNase 8, a novel RNase A superfamily ribonuclease expressed uniquely in placenta, Nucleic Acids Res 30(5):1169-1175, 2002.
10. Tang CY, Lu CL, Chang MDT et al., Constrained multiple sequence alignment tool development and its application to RNase family alignment, J Bioinformatics Comput Biol 1(2):267-287, 2003.
11. Welling GW, Weijer WJ, van der Zee R, Welling-Wester S, Prediction of sequential antigenic regions in proteins, FEBS Letts 188(2):215-218, 1985.
12. Stylos WA, Merryman CF, Maurer PH, Antigenicity of polypeptides (poly-alpha-amino acids). Distribution of sheep antibodies to polymers of alpha-L-amino acids of varying net electrical charge and lysozyme, Int Arch Allergy Appl Immunol 39(4): 381-390, 1970.
13. Mauere PH, Merryman CF, Stylos WA, Antigenicity of polypeptides (poly-alpha-amino acids). Distribution of sheep antibodies to dinitrinophenyl-(DNP) conjugates of polymers of alpha-L-amino acids of varying electrical charge, Int Arch Allergy Appl Immunol 39(4):435-444, 1970.
14. Jasin HE, Glynn LE, The antigenticity of some synthetic Poly-Iminoacids. I. Antigenic properties of Poly-L-Proline, Immunology 42:95-105, 1965.
15. Jasin HE, Glynn LE, The antigentic properties of some synthetic Poly-Iminoacids. II. The antigenicity of polypeptides related to collagen; peptides containing hydorxyproline and acetyl-hydroxy-proline, Immunology 32:260-269, 1965.
16. Watts TH, Sastry PA, Hodges RS, Paranchych W, Mapping of the antigenic determinants of Pseudomonas aeruginosa PAK polar pili, Infect Immun 42(1):113-121, 1983.
17. Collins EJ, Garboczi DN, Wiley Collins DC, Three-dimensional structure of a peptide extending from one end of a class I MHC binding site, Nature 371(6498):626-629, 1994.
18. Ruppert J et al., Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules, Cell 74(5):929-937, 1993.
19. Donnes P, Elofsson A, Prediction of MHC class I binding peptides, using SVMHC, BMC Bioinformatics 3(1):25, 2002.
20. Gulukota K et al., Two complementary methods for predicting peptides binding major histocompatibility complex molecules, J Mol Biol 267(5):1258-1267, 1997.
21. Dayhoff MO, Schwartz RM, Orcutt BC, A model of evolutionary change in proteins. matrices for detecting distant relationships, National biomedical research foundation, Washington DC, pp. 345-358.
22. Henikoff S, Henikoff JG, Amino acid substitution matrices from protein blocks, Proc Natl Acad Sci USA 89:10915-10919, 1992.
23. Voorhees EM, Implementing agglometrative hierarchical clustering algorithms for use in document retrieval, Information Processing & Management 22:465-476, 1986.
24. Boyer RS, Moore JS, A fast string searching algorithm, Commun ACM 20:762-772, 1977.
25. Younus H, Owais M, Rao DN, Saleemuddin M, Stabilization of pancreatic ribonuclease A by immobilization on Sepharose-linked antibodies that recognize the labile region of the enzyme, Biochim Biophys Acta 1548(1):114-120, 2001.
26. Plasterer TN, PROTEAN. Protein sequence analysis and prediction, Mol Biotech 16:117-126, 2000.
27. Boix E et al., Identification and characterization of human eosinophil cationic protein by an epitope-specific antibody, J Leukoc Biol 69(6):1027-1035, 2001.
28. Harlow E, Lane D, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, NY, 1988.