IsoSVM - Distinguishing isoforms and paralogs on the protein level

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Spitzer, Michael ^a   Lorkowski, Stefan ^a   Cullen, Paul ^a   Sczyrba, Alexander ^b   Fuellen, Georg ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOTETRAPLOID SPECIES; AUTOMATED APPROACH; DATABASE SEARCHES; LINEAR CLASSIFIERS; PHYLOGENETIC RECONSTRUCTION; PROTEIN SEQUENCES; PROTEOME DATABASE; VISUAL ANALYSIS;

DATABASE SYSTEMS; GENES; INFORMATION RETRIEVAL; PROTEINS; RADIAL BASIS FUNCTION NETWORKS; SEARCH ENGINES;

SUPPORT VECTOR MACHINES;

COMPLEMENTARY DNA; ISOPROTEIN; PROTEIN;

ACCESS TO INFORMATION; ACCURACY; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; NONHUMAN; ORTHOLOGY; PARALOGY; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; XENOPUS LAEVIS; ALGORITHM; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CHEMISTRY; CLASSIFICATION; EVALUATION; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

XENOPUS LAEVIS;

ALGORITHMS; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PROTEIN ISOFORMS; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 33645537946     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-110     Document Type: Article

References (37)

1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P: Molecular Biology of the Cell 4th edition. Garland Publishing, New York; 2000.
2. Graveley BR: Alternative splicing: increasing diversity in the proteomic world. Trends Genet 2001, 17(2):100-107.
3. Cartegni L, Chew SL, Krainer AR: Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nature Reviews Genetics 2002, 3:285-298.
4. Grabowski PJ, Black DL: Alternative RNA splicing in the nervous system. Prog Neurobiol 2001, 65(3):289-308.
5. Fitch WM: Distinguishing homologous from analogous proteins. Syst Zool 1970, 19(2):99-113.
6. Lee C, Atanelov L, Modrek B, Xing Y: ASAP: The Alternative Splicing Annotation Project. Nucl Acids Res 2003, 31:101-105.
7. Pospisil H, Herrmann A, Bortfeldt R, Reich J: EASED: Extended Alternatively Spliced EST Database. Nucl Acids Res 2004, 32:D70-74.
8. Thanaraj TA, Stamm S, Clark F, Riethoven JJM, Le Texier V, Muilu J: ASD: the Alternative Splicing Database. Nucl Acids Res 2004, 32:D64-D69.
9. Boser BE, Guyon IM, Vapnik VN: A training algorithm for optimal margin classifiers. 5th Annual ACM Workshop COLT 1992:144-152.
10. Cortes C, Vapnik V: Support vector networks. Machine Learning 1995, 20:273-297.
11. Schölkopf B, Smola AJ: Learning with Kernels MIT Press, Cambridge, MA: 2002.
12. Müller KR, Mika S, Rätsch G, Tsuda K, Schölkopf B: An Introduction to Kernel-based Learning Algorithms. IEEE Neural Networks 2001, 12(2):181-201.
13. Byvatov E, Schneider G: Support vector machine applications in bioinformatics. Appl Bioinformatics 2003, 2(2):67-77.
14. Zhang XH, Heller KA, Hefter I, Leslie CS, Chasin LA: Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. Genome Res 2003, 13(12):2637-2650.
15. Leslie CS, Eskin E, Cohen A, Weston J, Noble WS: Mismatch string kernels for discriminative protein classification. Bioinformatics 2004, 20(4):467-476.
16. Dror G, Sorek R, Shamir R: Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics 2005, 21(7):897-901.
17. Joachims T: Making large-Scale SVM Learning Practical. In Advances in Kernel Methods - Support Vector Learning Edited by: Schölkopf B, Burges C, Smola A. MIT-Press; 1999.
18. Fuellen G, Spitzer M, Cullen P, Lorkowski S: BLASTing proteomes, yielding phylogenies. In Silica Biol 2003, 3(3):313-319.
19. Fuellen G, Spitzer M, Cullen P, Lorkowski S: Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets. Proteins 2005, 61(4):888-899.
20. Moody J, Darken DJ: Fast learning in networks of locally-tuned processing units. Neural Computation 1989, 1(2):281-294.
21. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucl Acids Res 2005, 33:D39-D45.
22. Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R, Altmann CR: XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics 2005, 6:123.
23. Abouelhoda MI, Kurtz S, Ohlebusch E: Replacing Suffix Trees with Enhanced Suffix Arrays. Journal of Discrete Algorithms 2004, 2:53-86.
24. Vmatch [http://www.vmatch.de]
25. Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 1999, 9(9):868-877.
26. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997, 25:3389-3402.
27. Dean M, Rzhetsky A, Allikmets R: The human ATP-binding cassette (ABC) transporter superfamily. Genome Res 2001, 11(7):1156-1166.
28. IsoSVM [http://www.uni-muenster.de/Bioinformatics/services/isosvm/]
29. Hsu CW, Chang CC, Lin CJ: A practical guide to support vector classification. [http://www.csie.ntu.edu.tw/~cilin/].
30. Sarle WS: Neural Network FAQ. Periodic posting to the Usenet newsgroup comp.ai.neural-nets 1997.
31. Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acids Res 2002, 30:3059-3066.
32. Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8(3):275-282.
33. Fuellen G: A Gentle Guide to Multiple Alignment. Complexity International 1997, 4: [http://journal-ci.csse.monash.edu.au/ci/vo104/ mulali].
34. Brown NP, Leroy C, Sander C: MView: a web-compatible database search or multiple alignment viewer. Bioinformatics 1998, 14(4):380-381.
35. Qian J, Lin J, Luscombe NM, Yu H, Gerstein M: Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics 2003, 19(15):1917-1926.
36. Rätsch G, Onoda T, Müller K: Soft Margins for AdaBoost. Mach Learn 2001, 42(3):287-320.
37. Efron B, Gong G: A leisurely look at the bootstrap, the jackknife, and cross-validation. The American Statistician 1983, 37:36-48.