Improved phylogenetic motif detection using parsimony

Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

Volumn 2005, Issue , 2005, Pages 19-26

  Roshan, Usman ^a   Livesay, Dennis R ^b   La, David ^b  

^a NEW JERSEY INSTITUTE OF TECHNOLOGY   (United States)

^b CALIFORNIA STATE POLYTECHNIC UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATASETS; FUNCTIONAL SITES; PARSIMONY; PHYLOGENY;

ALGORITHMS; COMPUTATIONAL METHODS; DATA STRUCTURES; HEURISTIC METHODS; PROTEINS;

OBJECT RECOGNITION;

EID: 33751174062     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2005.38     Document Type: Conference Paper

References (27)

1. Jones S and Thornton JM. Searching for functional sites in protein structures. Curr Opin Chem Biol 8 (2004) pp:3-7.
2. La D and Livesay DR. Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics 6 (2005) pp: 116.
3. La D, Sutch B, and Livesay DR. Predicting protein functional sites with phylogenetic motifs. Proteins 58 (2005) pp:309-320.
4. Livesay DR and La D. The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins. Protein Sci 14 (2005) pp:1158-1170.
5. Lichtarge O, Bourne HR, and Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 251 (1996) pp:342-358.
6. Lichtarge O, Sowa ME, and Philippi A. Evolutionary traces of functional surfaces along G protein signaling pathway. Methods Enzymol 344 (2002) pp:536-556.
7. Lichtarge O, Yao H, Kristensen DM, Madabushi S, and Mihalek I. Accurate and scalable identification of functional sites by evolutionary tracing. J Struct Funct Genomics 4 (2003) pp:159-166.
8. Armon A, Graur D, and Ben Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 307 (2001) pp:447-463.
9. Bickel PJ, Kechris KJ, Spector PC, Wedemayer GJ, and Glazer AN. Finding important sites in protein sequences. Proc Natl Acad Sci USA 99 (2002) pp:14764-14771.
10. del Sol MA, Pazos F, and Valencia A. Automatic methods for predicting functionally important residues. J Mol Biol 326 (2003) pp: 1289-1302.
11. Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, Kimmel M, Kavraki L, and Lichtarge O. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol 326 (2003) pp:255-261.
12. Swofford DJ and Olsen GJ. Phytogeny reconstruction, Molecular Systematics. Hills D, Moritz C, Marble BK, eds Sinauer Ass. Inc. (1996) pp:407-514.
13. Foulds LR and Graham RL. The Steiner problem in phylogeny is NP-complete. Advances in Appled Math 3 (1982) pp:43-49.
14. Felsenstein J. PHYLIP - Phylogeny Inference Package [Version 3.2]. Cladistics 5 (1989) pp:164-166.
15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 (1987) pp:406-425.
16. Thompson JD, Higgins DO, and Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 (1994) pp:4673-4680.
17. Goloboff P. Analyzing large data sets in reasonable times: solution for composite optima. Cladistics 15 (1999) pp:415-428.
18. Roshan U, Moret BME, Warnow T, and Williams TL. Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees. Proceedings of the IEEE Computational Systems Bioinformatics conference [CSB]. Stanford, California (2004).
19. Robinson DF and Foulds LR. Comparison of phylogenetic trees. Math BioSci 53 (1981) pp:131-147.
20. Crooks GE, Hon G, Chandonia JM, and Brenner SE. WebLogo: a sequence logo generator. Genome Res 14 (2004) pp: 1188-1190.
21. Aloy P, Querol E, Aviles FX, and Sternberg MJ. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 311 (2001) pp:395-408.
22. Kursula I and Wierenga RK. Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution. J Biol Chem 278 (2003) pp:9544-9551.
23. Tellez-Valencia A, Olivares-Illana V, Heraandez-Santoyo A, Perez-Montfort R, Costas M, Rodriguez-Romero A, Lopez-Calahorra F, Tuena DG-P, and Gomez-Puyou A. Inactivation of triosephosphate isomerase from Trypanosoma cruzi by an agent that perturbs its dimer interface. J Mol Biol 341 (2004) pp:1355-1365.
24. La D and Livesay DR. MINER: Software for phylogenetic motif identification. Nucleic Acids Res (2005) in press.
25. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, and Natale DA. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4 (2003) pp:41.
26. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, and Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31 (2003) pp:365-370.
27. Hulo N, Sigrist CJ, Le S, V, Langendijk-Genevaux PS, Bordoli L, Gattiker A, De Castro E, Bucher P, and Bairoch A. Recent improvements to the PROSITE database. Nucleic Acids Res 32 Database issue (2004) pp:D134-D137.