Improved spliced alignment from an information theoretic approach

Bioinformatics

Volumn 22, Issue 1, 2006, Pages 13-20

  Zhang, Miao ^a,b   Gish, Warren ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; CAENORHABDITIS ELEGANS; COMPUTER PROGRAM; CONTROLLED STUDY; EXON; EXPRESSED SEQUENCE TAG; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RICE; RNA SEQUENCE; RNA SPLICING; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

ANIMALIA; CAENORHABDITIS ELEGANS; METAZOA;

EID: 30344435920     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti748     Document Type: Article

References (38)

1. Altschul,S.F. (1991) Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol., 219, 555-565.
2. Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
3. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
4. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
5. Bailey,L.C.,Jr et al. (1998) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res., 8, 362-376.
6. Bedell,J.A. et al. (2000) MaskerAid: A performance enhancement to RepeatMasker. Bioinformatics, 16, 1040-1041.
7. Berg,O.G. and von Hippel,P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
8. Black,D.L. (2000) Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell, 103, 367-370.
9. Brett,D. et al. (2000) EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett., 474, 83-86.
10. Buetow,K.H. et al. (1999) Reliable identification of large numbers of candidate SNPs from public EST data. Nat. Genet., 21, 323-325.
11. Burset,M. et al. (2000) Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res., 28, 4364-4375.
12. Delcher,A.L. et al. (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res., 30, 2478-2483.
13. Florea,L. et al. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
14. Florea,L. et al. (2005) Gene and alternative splicing annotation with AIR. Genome Res., 15, 54-66.
15. Jurka,J. (2000) Repbase update: A database and an electronic journal of repetitive elements. Trends Genet., 16, 418-420.
16. Kan,Z. et al. (2000) UTR reconstruction and analysis using genomically aligned EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 218-227.
17. Kan,Z. et al. (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res., 11., 889-900.
18. Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
19. Kent,W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
20. Ladd,A.N. and Cooper,T.A. (2002) Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol., 3, reviews0008.
21. Makalowski,W. and Boguski,M.S. (1998) Evolutionary parameters of the transcribed mammalian genome: In analysis of 2,820 orthologous rodent and human sequences. Proc. Natl Acad. Sci. USA, 91, 9407-9412.
22. Marth,G.T. et al. (1999) A general approach to single-nucleotide polymorphism discovery. Nat. Genet., 23, 452-456.
23. Mironov,A.A. et al. (1999) Frequent alternative splicing of human genes. Genome Res., 9, 1288-1293.
24. Modrek,B. et al. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res., 29, 2850-2859.
25. Mott,R. (1997) EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci., 13, 477-478.
26. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 433-453.
27. Picoult-Newberg,L. et al. (1999) Mining SNPs from EST databases. Genome Res., 9, 167-174.
28. Sankoff,D. and Kruskal,J.B. (1983) Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, Reading, MA.
29. Shannon,C.E. (1948) A mathematical theory of communication. Bell Syst. Tech. J., 27, 379-423.
30. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
31. Sokal,R.R. and Rohlf,F.J. (1995) Biometry. W. F. Freeman and Company: New York, NY.
32. States,D.J. et al. (1991) Improved sensitivity of nucleic acid database searches using application-specific scoring matrices. Methods, 3, 66-70.
33. Stormo,G.D. (1988) Computer methods for analyzing sequence recognition of nucleic acids. Annu. Rev. Biophys. Biophys. Chem., 17, 241-263.
34. Stormo,G.D. and Hartzell,G.W.,III (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA, 86, 1183-1187.
35. Usuka,J. et al. (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics. 16, 203-211.
36. Volfovsky,N. et al. (2003) Computational discovery of internal micro-exons. Genome Res., 13, 1216-1221.
37. Wheelan,S.J. et al. (2001) Spidey: A tool for mRNA-to-genomic alignments. Genome Res., 11, 1952-1957.
38. Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.