PSIST: A scalable approach to indexing protein structures using suffix trees

Journal of Parallel and Distributed Computing

Volumn 68, Issue 1, 2008, Pages 54-63

  Gao, Feng ^a   Zaki, Mohammed J ^a  

^a Rensselaer Polytechnic Institute   (United States)

Author keywords

Bioinformatics; External suffix trees; Protein structure indexing

Indexed keywords

BIOINFORMATICS; CLASSIFICATION (OF INFORMATION); DRUG DELIVERY; TOPOLOGY;

DRUG DISCOVERY; EXTERNAL SUFFIX TREES; FUNCTION PREDICTION; PROTEIN STRUCTURE INDEXING;

PROTEINS;

EID: 36649013506     PISSN: 07437315     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jpdc.2007.07.008     Document Type: Article

References (43)

1. Altschul S., Madden T., Schaffer A., Zhang J., Zhang Z., Miller W., and Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 17 (1997) 3389-3402
2. Aung Z., Fu W., and Tan K.L. An efficient index-based protein structure database searching method. International Conference on Database Systems for Advanced Applications (DASFAA) (2003) 311-318
3. Bhattacharya A., Can T., Kahveci T., Singh A.K., and Wang Y.F. ProGreSS: simultaneous searching of protein databases by sequence and structure. Pacific Symposium on Bioinformatics (2004) 264-275
4. Brenner S.E., Koehl P., and Levitt M. The ASTRAL compendium for sequence and structure analysis. Nucleic Acids Res. 28 (2000) 254-256
5. Çamoǧlu O., Kahveci T., and Singh A.K. Towards index-based similarity search for protein structure databases. IEEE Computer Society Bioinformatics Conference (CSB) (2003) 148-158
6. Can T., and Wang Y.F. CTSS: a robust and efficient method for protein structure alignment based on local geometrical and biological features. IEEE Computer Society Bioinformatics Conference (CSB) (2003) 169-179
7. Choi I., Kwon J., and Kim S. Local feature frequency profile: a method to measure structural similarity in proteins. Proc. Nat. Acad. Sci. U.S.A. 101 11 (2004) 3797-3802
8. Clifford R. Distributed suffix trees. J. Discrete Algorithms 3 2-4 (2005) 176-197
9. Dayhoff M.O., Schwartz R.M., and Orcutt B.C. A model of evolutionary change in proteins. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure (1978) 345-352
10. Delcher A.L., Kasif S., Fleischmann R.D., Peterson J., White O., and Salzberg S.L. Alignment of whole genomes. Nucleic Acid Res. 27 11 (1999) 2369-2376
11. Delcher A.L., Phillippy A., Carlton J., and Salzberg S.L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acid Res. 30 11 (2002) 2478-2483
12. Dror O., Benyamini H., Nussinov R., and Wolfson H. MASS: multiple structural alignment by secondary structures. Bioinformatics 19 12 (2003) 95-104
13. Eidhammer I., Jonassen I., and Taylor W.R. Structure comparison and structure patterns. J. Comput. Biol. 7 5 (2000) 685-716
14. Farach-Colton M., Ferragina P., and Muthukrishnan S. On the sorting-complexity of suffix tree construction. J. ACM 47 6 (2000) 987-1011
15. Gao F., and Zaki M.J. PSIST: indexing protein structures using suffix trees. IEEE Computational Systems Bioinformatics Conference (2005)
16. Gribskov M., and Robinson N. Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem. 20 (1996) 25-33
17. Gusfield D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology (1997), Cambridge University Press, New York
18. Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Nat. Acad. Sci. U.S.A. 89 22 (1992) 10915-10919
19. Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233 (1993) 123-138
20. Holm L., and Sander C. 3-D lookup: fast protein structure database searches at 90% reliability. International Conference on Intelligent Systems for Molecular Biology (ISMB) (1995) 179-187
21. Hunt E., Atkinson M., and Irving R. A database index to large biological sequences. International Conference on Very Large Data Bases (VLDB) (2001)
22. Hunt E., Atkinson M., and Irving R. Database indexing for large DNA and protein sequence collections. International Conference on Very Large Data Bases (VLDB) (2002) 256-271
23. Japp R. The top-compressed suffix tree. 21st Annual British National Conference on Databases (2004)
24. Lamdan Y., and Wolfson H.J. Geometric hashing: a general and efficient model-based recognition scheme. International Conference on Computer Vision (ICCV) (1988) 238-249
25. Madej T., Gibrat J.F., and Bryant S.H. Threading a database of protein cores. Proteins 23 (1995) 356-369
26. McCreight E.M. A space-economic suffix tree construction algorithm. J. ACM 23 2 (1976) 262-272
27. C. Meek, J.M. Patel, S. Kasetty, OASIS: an online and accurate technique for local-alignment searches on biological sequences, in: International Conference on Very Large Data Bases (VLDB), pp. 910-923.
28. Mizoguchi K., and Go N. Comparison of spatial arrangements of secondary structural elements in proteins. Protein Eng. 8 (1995) 353-362
29. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
30. Nussinov R., Leibowit N., and Wolfson H.J. MUSTA: a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins. J. Comput. Biol. 8 2 (2001) 93-121
31. Orengo C., Michie A., Jones S., Jones D., Swindells M., and Thornton J. CATH-a hierarchic classification of protein domain structures. Structure 5 8 (1997) 1093-1108
32. Orengo C.A., and Taylor W.R. SSAP: sequential structure alignment program for protein structure comparisons. Methods Enzymol. 266 (1996) 617-634
33. Pearl F., Todd I., Sillitoe A., Dibley M., Redfern O., Lewis T., Bennett C., Marsden R., Grant A., Lee D., Akpor A., Maibaum M., Harrison A., Dallman T., Reeves G., Diboun I., Addou S., Lise S., Johnston C., Sillero A., Thornton J., and Orengo C. The CATH domain structure database and related resources gene3d and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res. 33 (2005) 247-251
34. Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Nat. Acad. Sci. U.S.A. 85 (1988) 2444-2448
35. B. Phoophakdee, M.J. Zaki, TRELLIS: genome-scale disk-based suffix tree indexing, in: ACM SIGMOD International Conference on Management of Data, June 2007.
36. Rost B. Twilight zone of protein sequence alignments. Protein Eng. 12 2 (1999) 85-94
37. K.B. Schürmann, J. Stoye, Suffix tree construction and storage with limited main memory, Technical Report 0946-7831, Universität Bielefeld, 2003.
38. Shatsky M., Nussinov R., and Wolfson H.J. Multiprot-a multiple protein structural alignment algorithm. Proteins 56 (2004) 143-156
39. Shindyalov I.N., and Bourne P.E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11 9 (1998) 739-747
40. Tata S., Hankins R., and Patel J. Practical suffix tree construction. International Conference on Very Large Data Bases (VLDB) (2004) 36-47
41. Taubig H., Buchner A., and Griebsch J. A method for fast approximate searching of polypeptide structures in the PDB. German Conference on Bioinformatics (GCB) (2004)
42. Ukkonen E. On-line construction of suffix trees. Algorithmica 14 3 (1995) 249-260
43. Yuan X., and Bystroff C. Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics 21 7 (2005) 1010-1019