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Volumn 6, Issue 5, 2008, Pages 1021-1033

Finding alternative splicing patterns with strong support from expressed sequences on individual exons/introns

Author keywords

Alternative splicing pattern; ESTs; Expressed sequences

Indexed keywords

ARTICLE; DATA ANALYSIS SOFTWARE; EXON; EXPRESSED SEQUENCE TAG; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC DATABASE; HUMAN; INTRON; PREDICTION; RNA SPLICING; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS;

EID: 54049115762     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720008003825     Document Type: Article
Times cited : (4)

References (30)
  • 2
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander ES, Linton LM, Birren B et al., Initial sequencing and analysis of the human genome, Nature 409:860-921, 2001.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1    Linton, L.M.2    Birren, B.3
  • 3
    • 0342723790 scopus 로고    scopus 로고
    • Frequent alternative splicing of human genes
    • Mironov AA, Fickett JW, Gelfand MS, Frequent alternative splicing of human genes, Genome Res 9(12):1288-1293, 1999.
    • (1999) Genome Res , vol.9 , Issue.12 , pp. 1288-1293
    • Mironov, A.A.1    Fickett, J.W.2    Gelfand, M.S.3
  • 4
    • 14644412463 scopus 로고    scopus 로고
    • A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins
    • Sakabe NJ, Vibranovski MD, de Souza SJ, A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins, Genet Mol Res 3(4):532-544, 2004.
    • (2004) Genet Mol Res , vol.3 , Issue.4 , pp. 532-544
    • Sakabe, N.J.1    Vibranovski, M.D.2    de Souza, S.J.3
  • 5
    • 19844379515 scopus 로고    scopus 로고
    • Genome-wide assembly and analysis of alternative transcripts in mouse
    • Sharov AA, Dudekula DB, Ko MS, Genome-wide assembly and analysis of alternative transcripts in mouse, Genome Res 15:748-754, 2005.
    • (2005) Genome Res , vol.15 , pp. 748-754
    • Sharov, A.A.1    Dudekula, D.B.2    Ko, M.S.3
  • 6
    • 0031577732 scopus 로고    scopus 로고
    • Alternative splicing of fibroblast growth factor receptor 2 (FGF-R2) in human prostate cancer
    • Carstens RP, Eaton JV, Krigman HR, Walther PJ, Garcia-Blanco MA, Alternative splicing of fibroblast growth factor receptor 2 (FGF-R2) in human prostate cancer, Oncogene 15:3059-3065, 1997.
    • (1997) Oncogene , vol.15 , pp. 3059-3065
    • Carstens, R.P.1    Eaton, J.V.2    Krigman, H.R.3    Walther, P.J.4    Garcia-Blanco, M.A.5
  • 7
    • 0033564485 scopus 로고    scopus 로고
    • Molecular cloning and expression of an alternative hKLK3 transcript coding for a variant protein of prostate-specific antigen
    • Henze N, Olayat S, Gutman N, Zani ML, Courty Y, Molecular cloning and expression of an alternative hKLK3 transcript coding for a variant protein of prostate-specific antigen, Cancer Res 59 2820-2824, 1999.
    • (1999) Cancer Res , vol.59 , pp. 2820-2824
    • Henze, N.1    Olayat, S.2    Gutman, N.3    Zani, M.L.4    Courty, Y.5
  • 8
    • 0141974926 scopus 로고    scopus 로고
    • Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences
    • Xu Q, Lee C, Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences, Nucleic Acids Res 31(19): 5635-5643, 2003.
    • (2003) Nucleic Acids Res , vol.31 , Issue.19 , pp. 5635-5643
    • Xu, Q.1    Lee, C.2
  • 9
    • 0037350957 scopus 로고    scopus 로고
    • SLAM: Cross-species gene finding and alignment with a generalized pair hidden Maxkov model
    • Alexandersson M. Cawley S, Pachter L, SLAM: Cross-species gene finding and alignment with a generalized pair hidden Maxkov model, Genome Res 13(3):496-502, 2003.
    • (2003) Genome Res , vol.13 , Issue.3 , pp. 496-502
    • Alexandersson, M.1    Cawley, S.2    Pachter, L.3
  • 10
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge C, Karlin S, Prediction of complete gene structures in human genomic DNA, J Mol Biol 268:78-94, 2004.
    • (2004) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 11
    • 38949107416 scopus 로고    scopus 로고
    • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events
    • Holste D, Ohler U, Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events, PLoS Comput Biol 4(1):e21, 2008.
    • (2008) PLoS Comput Biol , vol.4 , Issue.1
    • Holste, D.1    Ohler, U.2
  • 12
    • 0034066018 scopus 로고    scopus 로고
    • Using database matches with HMMGene for automated gene detection in Drosphila
    • Krogh A, Using database matches with HMMGene for automated gene detection in Drosphila, Genome Res 10(4):391-397, 2000.
    • (2000) Genome Res , vol.10 , Issue.4 , pp. 391-397
    • Krogh, A.1
  • 13
    • 33747830848 scopus 로고    scopus 로고
    • Stanke M, Keller O, Gundu I, Waack S, Hayes A, Morgenstern B, AUGUSTUS: Ab initio prediction of alternative transcripts, Nucleic Acids Res 34:W435-W439, 2006.
    • Stanke M, Keller O, Gundu I, Waack S, Hayes A, Morgenstern B, AUGUSTUS: Ab initio prediction of alternative transcripts, Nucleic Acids Res 34:W435-W439, 2006.
  • 15
    • 25444512373 scopus 로고    scopus 로고
    • Integrating alternative splicing detection into gene prediction
    • Foissac S, Schiex T, Integrating alternative splicing detection into gene prediction, BMC Bioinformatics 6:25, 2005.
    • (2005) BMC Bioinformatics , vol.6 , pp. 25
    • Foissac, S.1    Schiex, T.2
  • 16
    • 2442709350 scopus 로고    scopus 로고
    • Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs
    • Grasso C, Modrek B, Xing Y, Lee C, Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs, Pac Symp Biocomput, pp. 29-41, 2004.
    • (2004) Pac Symp Biocomput , pp. 29-41
    • Grasso, C.1    Modrek, B.2    Xing, Y.3    Lee, C.4
  • 17
    • 0037606127 scopus 로고    scopus 로고
    • Generating consensus sequences from partial order multiple sequence alignment graphs
    • Lee C, Generating consensus sequences from partial order multiple sequence alignment graphs, Bioinformatics 19:999-1008, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 999-1008
    • Lee, C.1
  • 18
    • 33748770921 scopus 로고    scopus 로고
    • Bioinformatics of alternative splicing and its regulation
    • Florea L, Bioinformatics of alternative splicing and its regulation, Brief Bioinform 7:55-69, 2006.
    • (2006) Brief Bioinform , vol.7 , pp. 55-69
    • Florea, L.1
  • 19
    • 27644510938 scopus 로고    scopus 로고
    • ASPIC: A novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences
    • Bonizzoni P, Rizzi R, Pesole G, ASPIC: A novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences, BMC Bioinformatics 6:244, 2005.
    • (2005) BMC Bioinformatics , vol.6 , pp. 244
    • Bonizzoni, P.1    Rizzi, R.2    Pesole, G.3
  • 20
    • 2442700175 scopus 로고    scopus 로고
    • ESTGenes: Alternative splicing from ESTs in Ensembl
    • Eyras E, Caccamo M, Curwen V, Clamp M, ESTGenes: Alternative splicing from ESTs in Ensembl, Genome Res 14:976-987, 2004.
    • (2004) Genome Res , vol.14 , pp. 976-987
    • Eyras, E.1    Caccamo, M.2    Curwen, V.3    Clamp, M.4
  • 23
    • 17844407888 scopus 로고    scopus 로고
    • ECgene: Genome-based EST clustering and gene modeling for alternative splicing
    • Kim N, Shin S, Lee S, ECgene: Genome-based EST clustering and gene modeling for alternative splicing, Genome Res 15:566-576, 2005.
    • (2005) Genome Res , vol.15 , pp. 566-576
    • Kim, N.1    Shin, S.2    Lee, S.3
  • 24
    • 3843111257 scopus 로고    scopus 로고
    • The Alternative Splicing Gallery (ASG): Bridging the gap between. genome and transcriptome
    • Leipzig J, Pevzner P, Heber S, The Alternative Splicing Gallery (ASG): Bridging the gap between. genome and transcriptome, Nucleic Acids Res 32:3977-3983, 2004.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3977-3983
    • Leipzig, J.1    Pevzner, P.2    Heber, S.3
  • 26
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • Kent WJ, BLAT - The BLAST-like alignment tool, Genome Res 12 656-664, 2002.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 27
    • 0002430769 scopus 로고    scopus 로고
    • SpliceNest: Visualization of gene structure and alternative splicing based on EST clusters
    • Coward E, Haas SA, Vingron IM, SpliceNest: Visualization of gene structure and alternative splicing based on EST clusters, Trends Genet 18(1):53-55, 2002.
    • (2002) Trends Genet , vol.18 , Issue.1 , pp. 53-55
    • Coward, E.1    Haas, S.A.2    Vingron, I.M.3
  • 28
    • 4444270781 scopus 로고    scopus 로고
    • Genonie wide identification and classification of alternative splicing based on EST data
    • Gupta S, Zink D, Korn B, Vingron M, Haas SA. Genonie wide identification and classification of alternative splicing based on EST data. Bioinformatics 20:2579-2585, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 2579-2585
    • Gupta, S.1    Zink, D.2    Korn, B.3    Vingron, M.4    Haas, S.A.5
  • 29
    • 18744383071 scopus 로고    scopus 로고
    • A genomic mapping and alignment program for mRNA and EST sequences
    • Wu TD, Watanabe CK, GMAP: A genomic mapping and alignment program for mRNA and EST sequences, Bioinformatics 21:1859-1875, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe2    CK, G.M.A.P.3
  • 30
    • 33846036722 scopus 로고    scopus 로고
    • The ASAP II database: Analysis and comparative genomics of alternative splicing in 15 animal species
    • Database issue:D93-D98
    • Kim N, Alekseyenko AV, Roy M, Lee C, The ASAP II database: Analysis and comparative genomics of alternative splicing in 15 animal species, Nucleic Acids Res 35(Database issue):D93-D98, 2007.
    • (2007) Nucleic Acids Res , vol.35
    • Kim, N.1    Alekseyenko, A.V.2    Roy, M.3    Lee, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.