메뉴 건너뛰기




Volumn , Issue , 2009, Pages 847-852

Ab initio exon definition using an information theory-based approach

Author keywords

Biological system modeling; Genetics; Information theory; Monte carlo methods

Indexed keywords

AB INITIO; BIOLOGICAL MECHANISMS; BIOLOGICAL SYSTEM MODELING; DATA SETS; DONOR AND ACCEPTOR; GENETICS; RELATIVE ABUNDANCE; SHANNON INFORMATION THEORY; SPLICE SITE;

EID: 70349881775     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CISS.2009.5054835     Document Type: Conference Paper
Times cited : (2)

References (33)
  • 1
    • 0028895417 scopus 로고
    • Exon recognition in vertebrate splicing
    • Berget, S. M. "Exon recognition in vertebrate splicing," J. Biol. Chem, 270: 2411-2414, 1995.
    • (1995) J. Biol. Chem , vol.270 , pp. 2411-2414
    • Berget, S.M.1
  • 2
    • 1842635464 scopus 로고    scopus 로고
    • Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression
    • Zheng ZM. "Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression," J. Biomed Sci. 11:278-94, 2004.
    • (2004) J. Biomed Sci , vol.11 , pp. 278-294
    • Zheng, Z.M.1
  • 3
    • 70349885881 scopus 로고    scopus 로고
    • Moore, M. J., Query, C. C., Sharp, P. A in The RNA World (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), 303-358, 1993.
    • Moore, M. J., Query, C. C., Sharp, P. A in The RNA World (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), 303-358, 1993.
  • 6
    • 0028556367 scopus 로고
    • Dynamic RNA-RNA interactions in the splicesome
    • Madhani, H. D., Guthrie, C., "Dynamic RNA-RNA interactions in the splicesome," Annu. Rev. Genet, 28:1-26, 1994.
    • (1994) Annu. Rev. Genet , vol.28 , pp. 1-26
    • Madhani, H.D.1    Guthrie, C.2
  • 7
    • 0000882253 scopus 로고
    • Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein
    • Steitz, J.A., Black, D.L., Gerke, V., Parker, K.A., Kramer, A. Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein Particles, 115-154, 1988.
    • (1988) Particles , vol.115-154
    • Steitz, J.A.1    Black, D.L.2    Gerke, V.3    Parker, K.A.4    Kramer, A.5
  • 8
    • 0024062611 scopus 로고    scopus 로고
    • Seraphin, B., Kretzner, L., Rosbash, M. A. A Ul snRNA: pre-mRNA base pairing interaction is required early in yeast splicesome assembly but does not uniquely define the 5′ cleavage site, EMBO J., 7:2533-2538, 1988.
    • Seraphin, B., Kretzner, L., Rosbash, M. A. A Ul "snRNA: pre-mRNA base pairing interaction is required early in yeast splicesome assembly but does not uniquely define the 5′ cleavage site," EMBO J., 7:2533-2538, 1988.
  • 9
    • 0022550119 scopus 로고
    • A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation
    • Zhuang, Y., Weiner, A.M. "A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation," Cell, 46 (1986), 827-835
    • (1986) Cell , vol.46 , pp. 827-835
    • Zhuang, Y.1    Weiner, A.M.2
  • 10
    • 0023663370 scopus 로고
    • Recognitioin of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA
    • Parker, R., Siliciano, P. G., Guthrie, C. "Recognitioin of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA," Cell, 49 (1987), 229-239.
    • (1987) Cell , vol.49 , pp. 229-239
    • Parker, R.1    Siliciano, P.G.2    Guthrie, C.3
  • 11
    • 0024743838 scopus 로고
    • Mammalian pre-mRNA branch site selection by U2 snRNP involves base pairing
    • Wu, J. A., Manley, J. L. "Mammalian pre-mRNA branch site selection by U2 snRNP involves base pairing," Genes Dev., 3 (1989), 1553-1561
    • (1989) Genes Dev , vol.3 , pp. 1553-1561
    • Wu, J.A.1    Manley, J.L.2
  • 12
    • 0038070292 scopus 로고    scopus 로고
    • Information theory-based analysis of CYP2C19, CYP2D6, and CYP3A5 splicing mutations
    • Rogan PK, Svojanovsky SR, Leeder JS. "Information theory-based analysis of CYP2C19, CYP2D6, and CYP3A5 splicing mutations," Pharmacogenetics 13:207-218, 2003.
    • (2003) Pharmacogenetics , vol.13 , pp. 207-218
    • Rogan, P.K.1    Svojanovsky, S.R.2    Leeder, J.S.3
  • 13
    • 84856043672 scopus 로고
    • Mathematical Theory of Communication
    • Shannon, C.E. "Mathematical Theory of Communication," Bell Systems Tech. J. 27:379-623, 1948.
    • (1948) Bell Systems Tech. J , vol.27 , pp. 379-623
    • Shannon, C.E.1
  • 14
    • 0023042012 scopus 로고
    • Information content of binding sites on nucleotide sequences
    • Schneider TD, G. D. Stormo, L. Gold, and A. Ehrenfeucht. "Information content of binding sites on nucleotide sequences," J. Mol. Biol., 188, 415-431, 1986.
    • (1986) J. Mol. Biol , vol.188 , pp. 415-431
    • Schneider, T.D.1    Stormo, G.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 15
    • 2942610553 scopus 로고    scopus 로고
    • HMM sampling and applications to gene finding and alternative splicing
    • Cawley S and Pachter L. "HMM sampling and applications to gene finding and alternative splicing," Bioinformatics, 19S:36-41, 2003.
    • (2003) Bioinformatics , vol.19 S , pp. 36-41
    • Cawley, S.1    Pachter, L.2
  • 16
    • 0027054380 scopus 로고
    • Features of spliceome evolution and function inferred from an analysis of the information at human splice sites
    • Stephens R and T. D. Schneider. "Features of spliceome evolution and function inferred from an analysis of the information at human splice sites," J. Mol. Biol., 228: 1124-1136, 1992
    • (1992) J. Mol. Biol , vol.228 , pp. 1124-1136
    • Stephens, R.1    Schneider, T.D.2
  • 17
    • 0031583033 scopus 로고    scopus 로고
    • Information content of individual genetic sequences
    • Schneider T. D. "Information content of individual genetic sequences," J. Theor. Biol. 189(4): 427-441, 1997.
    • (1997) J. Theor. Biol , vol.189 , Issue.4 , pp. 427-441
    • Schneider, T.D.1
  • 18
    • 0029791403 scopus 로고    scopus 로고
    • Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information
    • Hebsgaard SM, Korning PG, Tolstrup N., Engelbrecht J., Rouze P., S. Brunak. "Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information," Nucleic Acids Res. 24:3439-3452, 1996.
    • (1996) Nucleic Acids Res , vol.24 , pp. 3439-3452
    • Hebsgaard, S.M.1    Korning, P.G.2    Tolstrup, N.3    Engelbrecht, J.4    Rouze, P.5    Brunak, S.6
  • 19
    • 4644319241 scopus 로고    scopus 로고
    • Bipartite pattern discovery by entropy minimization-based multiple local alignment
    • Bi C. and P.K. Rogan, "Bipartite pattern discovery by entropy minimization-based multiple local alignment," Nucleic Acids Res, 32:4979-91, 2004.
    • (2004) Nucleic Acids Res , vol.32 , pp. 4979-4991
    • Bi, C.1    Rogan, P.K.2
  • 21
    • 33644771267 scopus 로고    scopus 로고
    • BIPAD: A web server for modeling bipartite sequence elements
    • Bi C and Rogan PK, "BIPAD: a web server for modeling bipartite sequence elements," BMC Bioinformatics 7:76, 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. 76
    • Bi, C.1    Rogan, P.K.2
  • 22
    • 70349882564 scopus 로고    scopus 로고
    • www.ncbi.nlm.nih.gov/genome/guide/human/release-notes.html#b36
  • 25
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • Pietrovsky S. "Searching databases of conserved sequence regions by aligning protein multiple-alignments." Nucleic Acids Res. 24(21):4372, 1996.
    • (1996) Nucleic Acids Res , vol.24 , Issue.21 , pp. 4372
    • Pietrovsky, S.1
  • 26
    • 0031880376 scopus 로고    scopus 로고
    • Information analysis of human splice site mutations
    • Rogan PK, Faux B., Schneider TD, "Information analysis of human splice site mutations," Hum. Mut. 12:153-71, 1998.
    • (1998) Hum. Mut , vol.12 , pp. 153-171
    • Rogan, P.K.1    Faux, B.2    Schneider, T.D.3
  • 27
    • 10744223717 scopus 로고    scopus 로고
    • Two essential splice lariat branchpoint sequences in one intron in a xeroderma pigmentosum DNA repair gene: Mutations result in reduced XPC mRNA levels that correlate with cancer risk
    • Khan SG, Metin A., Gozukara E., Inui H., Shahlavi T., Muniz-Medina V., Baker CC, Ueda T., Aiken JR, Schneider TD, Kraemer KH. "Two essential splice lariat branchpoint sequences in one intron in a xeroderma pigmentosum DNA repair gene: mutations result in reduced XPC mRNA levels that correlate with cancer risk," Hum Mol Genet. 13:343-52, 2004.
    • (2004) Hum Mol Genet , vol.13 , pp. 343-352
    • Khan, S.G.1    Metin, A.2    Gozukara, E.3    Inui, H.4    Shahlavi, T.5    Muniz-Medina, V.6    Baker, C.C.7    Ueda, T.8    Aiken, J.R.9    Schneider, T.D.10    Kraemer, K.H.11
  • 28
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • Yeo G and Burge C., "Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals," J. Comput. Biol. 11:377-94, 2004.
    • (2004) J. Comput. Biol , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.2
  • 29
    • 17144362174 scopus 로고    scopus 로고
    • Automated splicing mutation analysis by information theory
    • Nalla V and Rogan PK, "Automated splicing mutation analysis by information theory," Hum. Mut. 25:334-42, 2005.
    • (2005) Hum. Mut , vol.25 , pp. 334-342
    • Nalla, V.1    Rogan, P.K.2
  • 30
    • 0032104509 scopus 로고    scopus 로고
    • Finding the genes in genomic DNA
    • Burge C and Karlin S. "Finding the genes in genomic DNA," Curr Opin Struct Bio. 8:346-354, 1998.
    • (1998) Curr Opin Struct Bio , vol.8 , pp. 346-354
    • Burge, C.1    Karlin, S.2
  • 31
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding,
    • Lukashin AV and Borodovsky M. "GeneMark.hmm: new solutions for gene finding,", Nucleic Acids Res. 26:1107-15, 1998.
    • (1998) Nucleic Acids Res , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 33
    • 0036207384 scopus 로고    scopus 로고
    • Listening to silence and understanding nonsense: Exonic mutations that affect splicing
    • Cartegni L., Chew S., Krainer AR, "Listening to silence and understanding nonsense: exonic mutations that affect splicing," Nat Rev. Genet. 3:285-98, 2002.
    • (2002) Nat Rev. Genet , vol.3 , pp. 285-298
    • Cartegni, L.1    Chew, S.2    Krainer, A.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.