메뉴 건너뛰기




Volumn 24, Issue 21, 2008, Pages 2438-2444

Direct mapping and alignment of protein sequences onto genomic sequence

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; COMPLEMENTARY DNA; PROTEIN;

EID: 54949090429     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn460     Document Type: Article
Times cited : (50)

References (57)
  • 1
    • 24644485994 scopus 로고    scopus 로고
    • JIGSAW: Integration of multiple sources of evidence for gene prediction
    • Allen,J.E. and Salzberg,S.L. (2005) JIGSAW: Integration of multiple sources of evidence for gene prediction. Bioinformatics, 21, 3596-3603.
    • (2005) Bioinformatics , vol.21 , pp. 3596-3603
    • Allen, J.E.1    Salzberg, S.L.2
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • 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.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 3
    • 0030628597 scopus 로고    scopus 로고
    • Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison
    • Birney,E. and Durbin,R. (1997) Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison. ISMB, 5, 56-64.
    • (1997) ISMB , vol.5 , pp. 56-64
    • Birney, E.1    Durbin, R.2
  • 4
    • 2442713832 scopus 로고    scopus 로고
    • GeneWise and genomewise
    • Birney,E. et al. (2004) GeneWise and genomewise. Genome Res. 14, 988-995.
    • (2004) Genome Res , vol.14 , pp. 988-995
    • Birney, E.1
  • 5
    • 0029056051 scopus 로고
    • Detection of new genes in a bacterial genome using Markov models for three gene classes
    • Borodovsky,M. et al. (1995) Detection of new genes in a bacterial genome using Markov models for three gene classes. Nucleic Acids Res. 23, 3554-3562.
    • (1995) Nucleic Acids Res , vol.23 , pp. 3554-3562
    • Borodovsky, M.1
  • 6
    • 29144445262 scopus 로고    scopus 로고
    • ExonHunter: A comprehensive approach to gene finding
    • Brejova,B. et al. (2005) ExonHunter: A comprehensive approach to gene finding. Bioinformatics, 21 (Suppl. 1), i57-i65.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Brejova, B.1
  • 7
    • 19944414942 scopus 로고    scopus 로고
    • Optimizing multiple seeds for protein homology search
    • Brown,D.G. (2005) Optimizing multiple seeds for protein homology search. IEEE/ACM Trans. Comput. Biol. Bioinform., 2, 29-38.
    • (2005) IEEE/ACM Trans. Comput. Biol. Bioinform , vol.2 , pp. 29-38
    • Brown, D.G.1
  • 8
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction programs
    • Burset,M. and Guigo,R. (1996) Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
    • (1996) Genomics , vol.34 , pp. 353-367
    • Burset, M.1    Guigo, R.2
  • 9
    • 0036677673 scopus 로고    scopus 로고
    • Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices
    • Cannata,N. et al. (2002) Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices. Bioinformatics, 18, 1102-1108.
    • (2002) Bioinformatics , vol.18 , pp. 1102-1108
    • Cannata, N.1
  • 10
    • 34347389905 scopus 로고    scopus 로고
    • Three distinct modes of intron dynamics in the evolution of eukaryotes
    • Carmel,L. et al. (2007) Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res., 17, 1034-1044.
    • (2007) Genome Res , vol.17 , pp. 1034-1044
    • Carmel, L.1
  • 11
    • 33745051802 scopus 로고    scopus 로고
    • Reference based annotation with GeneMapper
    • Chatterji,S. and Pachter,L. (2006) Reference based annotation with GeneMapper. Genome Biol., 7, R29.
    • (2006) Genome Biol , vol.7
    • Chatterji, S.1    Pachter, L.2
  • 12
    • 3843113189 scopus 로고    scopus 로고
    • Origins of recently gained introns in Caenorhabditis
    • Coghlan,A. andWolfe,K.H. (2004) Origins of recently gained introns in Caenorhabditis. Proc. Natl Acad. Sci. USA, 101, 11362-11367.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 11362-11367
    • Coghlan, A.1    andWolfe, K.H.2
  • 13
    • 34547852257 scopus 로고    scopus 로고
    • Homology search for genes
    • Cui,X. et al. (2007) Homology search for genes. Bioinformatics 23, i97-i103.
    • (2007) Bioinformatics , vol.23
    • Cui, X.1
  • 14
    • 2442707676 scopus 로고    scopus 로고
    • The Ensembl automatic gene annotation system
    • Curwen,V. et al. (2004) The Ensembl automatic gene annotation system. Genome Res., 14, 942-950.
    • (2004) Genome Res , vol.14 , pp. 942-950
    • Curwen, V.1
  • 15
    • 0003552989 scopus 로고
    • A model of evolutionary change in proteins, ed, National Biomedical Research Foundation, Silver Spring, ML, pp
    • Dayhoff,M.O. et al. (1978) A model of evolutionary change in proteins. In Dayhoff,M.O (ed.) Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Silver Spring, ML, pp. 345-352.
    • (1978) Atlas of Protein Sequence and Structure , pp. 345-352
    • Dayhoff, M.O.1
  • 16
    • 34548390530 scopus 로고    scopus 로고
    • Conrad: Gene prediction using conditional random fields
    • DeCaprio,D. et al. (2007) Conrad: Gene prediction using conditional random fields. Genome Res., 17, 1389-1398.
    • (2007) Genome Res , vol.17 , pp. 1389-1398
    • DeCaprio, D.1
  • 17
    • 1242320272 scopus 로고    scopus 로고
    • Local homology recognition and distance measures in linear time using compressed amino acid alphabets
    • Edgar,R.C. (2004) Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res. 32, 380-385.
    • (2004) Nucleic Acids Res , vol.32 , pp. 380-385
    • Edgar, R.C.1
  • 18
    • 0029830044 scopus 로고    scopus 로고
    • Gene recognition via spliced sequence alignment
    • Gelfand,M.S. et al. (1996) Gene recognition via spliced sequence alignment. Proc. Natl Acad. Sci. USA, 93, 9061-9066.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 9061-9066
    • Gelfand, M.S.1
  • 19
    • 33846659488 scopus 로고    scopus 로고
    • Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST
    • Gertz,E.M. et al. (2006) Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST. BMC Biol., 4, 41.
    • (2006) BMC Biol , vol.4 , pp. 41
    • Gertz, E.M.1
  • 20
    • 0031760236 scopus 로고    scopus 로고
    • Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes
    • Gotoh,O. (1998) Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes. Mol. Biol. Evol., 15, 1447-1459.
    • (1998) Mol. Biol. Evol , vol.15 , pp. 1447-1459
    • Gotoh, O.1
  • 21
    • 0034129662 scopus 로고    scopus 로고
    • Homology-based gene structure prediction: Simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps
    • Gotoh,O. (2000) Homology-based gene structure prediction: Simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. Bioinformatics, 16, 190-202.
    • (2000) Bioinformatics , vol.16 , pp. 190-202
    • Gotoh, O.1
  • 22
    • 43349092271 scopus 로고    scopus 로고
    • A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
    • Gotoh,O. (2008) A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. Nucleic Acids Res., 36, 2630-2638.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2630-2638
    • Gotoh, O.1
  • 23
    • 40449115745 scopus 로고    scopus 로고
    • CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction
    • Gross,S.S. et al. (2007) CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol., 8, R269.
    • (2007) Genome Biol , vol.8
    • Gross, S.S.1
  • 24
    • 0033782834 scopus 로고    scopus 로고
    • An assessment of gene prediction accuracy in large DNA sequences
    • Guigo,R. et al. (2000) An assessment of gene prediction accuracy in large DNA sequences. Genome Res., 10, 1631-1642.
    • (2000) Genome Res , vol.10 , pp. 1631-1642
    • Guigo, R.1
  • 25
    • 33748641351 scopus 로고    scopus 로고
    • EGASP: The human ENCODE genome annotation assessment project, Suppl. 1, S2 1-31
    • Guigo,R. et al. (2006) EGASP: The human ENCODE genome annotation assessment project. Genome Biol., 7 (Suppl. 1), S2 1-31.
    • (2006) Genome Biol , vol.7
    • Guigo, R.1
  • 26
    • 42949086676 scopus 로고    scopus 로고
    • Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments
    • Haas,B.J. et al. (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol., 9, R7.
    • (2008) Genome Biol , vol.9
    • Haas, B.J.1
  • 27
    • 0028303880 scopus 로고
    • An algorithm combining DNA and protein alignment
    • Hein,J. (1994) An algorithm combining DNA and protein alignment. J. Theor. Biol., 167, 169-174.
    • (1994) J. Theor. Biol , vol.167 , pp. 169-174
    • Hein, J.1
  • 28
    • 33747826336 scopus 로고    scopus 로고
    • GeneAlign: A coding exon prediction tool based on phylogenetical comparisons
    • Hsieh,S.J. et al. (2006) GeneAlign: A coding exon prediction tool based on phylogenetical comparisons. Nucleic Acids Res., 34, W280-W284.
    • (2006) Nucleic Acids Res , vol.34
    • Hsieh, S.J.1
  • 29
    • 0030446464 scopus 로고    scopus 로고
    • Methods for comparing a DNA sequence with a protein sequence
    • Huang,X. and Zhang,J. (1996) Methods for comparing a DNA sequence with a protein sequence. Comput. Appl. Biosci., 12, 497-506.
    • (1996) Comput. Appl. Biosci , vol.12 , pp. 497-506
    • Huang, X.1    Zhang, J.2
  • 30
    • 0031573382 scopus 로고    scopus 로고
    • A tool for analyzing and annotating genomic sequences
    • Huang,X. et al. (1997) A tool for analyzing and annotating genomic sequences. Genomics, 46, 37-45.
    • (1997) Genomics , vol.46 , pp. 37-45
    • Huang, X.1
  • 31
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature, 431, 931-945.
    • (2004) Nature , vol.431 , pp. 931-945
  • 32
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones,D.T. et al. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
    • (1992) Comput. Appl. Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1
  • 33
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 35
    • 0036202921 scopus 로고    scopus 로고
    • PatternHunter: Faster and more sensitive homology search
    • Ma,B. et al. (2002) PatternHunter: Faster and more sensitive homology search. Bioinformatics, 18, 440-445.
    • (2002) Bioinformatics , vol.18 , pp. 440-445
    • Ma, B.1
  • 36
    • 29244442741 scopus 로고    scopus 로고
    • Genome sequencing and analysis of Aspergillus oryzae
    • Machida,M. et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature, 438, 1157-1161.
    • (2005) Nature , vol.438 , pp. 1157-1161
    • Machida, M.1
  • 37
    • 1342263801 scopus 로고    scopus 로고
    • Gene structure conservation aids similarity based gene prediction
    • Meyer,I.M. and Durbin,R. (2004) Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res., 32, 776-783.
    • (2004) Nucleic Acids Res , vol.32 , pp. 776-783
    • Meyer, I.M.1    Durbin, R.2
  • 38
    • 0024236865 scopus 로고
    • Sequence comparison with concave weighting functions
    • Miller,W. and Myers,E.W. (1988) Sequence comparison with concave weighting functions. Bull. Math. Biol., 50, 97-120.
    • (1988) Bull. Math. Biol , vol.50 , pp. 97-120
    • Miller, W.1    Myers, E.W.2
  • 39
    • 0001338954 scopus 로고    scopus 로고
    • Simplified amino acid alphabets for protein fold recognition and implications for folding
    • Murphy,L.R. et al. (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng. 13, 149-152.
    • (2000) Protein Eng , vol.13 , pp. 149-152
    • Murphy, L.R.1
  • 40
    • 14044252770 scopus 로고    scopus 로고
    • Patterns of intron gain and loss in fungi
    • Nielsen,C.B. et al. (2004) Patterns of intron gain and loss in fungi. PLoS Biol., 2, e422.
    • (2004) PLoS Biol , vol.2
    • Nielsen, C.B.1
  • 41
    • 0041695455 scopus 로고    scopus 로고
    • Five hundred sixty-five triples of chicken, human, and mouse candidate orthologs
    • Ouyang,M, et al. (2003) Five hundred sixty-five triples of chicken, human, and mouse candidate orthologs. J. Mol. Evol., 57, 271-281.
    • (2003) J. Mol. Evol , vol.57 , pp. 271-281
    • Ouyang, M.1
  • 42
    • 0033381623 scopus 로고    scopus 로고
    • Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
    • Pavy,N. et al. (1999) Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences. Bioinformatics, 15, 887-899.
    • (1999) Bioinformatics , vol.15 , pp. 887-899
    • Pavy, N.1
  • 43
    • 0031573415 scopus 로고    scopus 로고
    • Comparison of DNA sequences with protein sequences
    • Pearson,W.R. et al. (1997) Comparison of DNA sequences with protein sequences. Genomics, 46, 24-36.
    • (1997) Genomics , vol.46 , pp. 24-36
    • Pearson, W.R.1
  • 44
    • 0022609080 scopus 로고
    • Algorithms for the search of amino acid patterns in nucleic acid sequences
    • Peltola,H. et al. (1986) Algorithms for the search of amino acid patterns in nucleic acid sequences. Nucleic Acids Res., 14, 99-107.
    • (1986) Nucleic Acids Res , vol.14 , pp. 99-107
    • Peltola, H.1
  • 45
    • 0035002807 scopus 로고    scopus 로고
    • Evaluation of gene-finding programs on mammalian sequences
    • Rogic,S. et al. (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res., 11, 817-832.
    • (2001) Genome Res , vol.11 , pp. 817-832
    • Rogic, S.1
  • 46
    • 0030869663 scopus 로고    scopus 로고
    • A method for identifying splice sites and translational start sites in eukaryotic mRNA
    • Salzberg,S.L. (1997) A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci. 13, 365-376.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 365-376
    • Salzberg, S.L.1
  • 47
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater,G.S. and Birney,E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 48
    • 3242889577 scopus 로고    scopus 로고
    • AUGUSTUS: A web server for gene finding in eukaryotes
    • Stanke,M. et al. (2004) AUGUSTUS: A web server for gene finding in eukaryotes. Nucleic Acids Res., 32, W309-W312.
    • (2004) Nucleic Acids Res , vol.32
    • Stanke, M.1
  • 49
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative
    • The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 50
    • 0032509302 scopus 로고    scopus 로고
    • The C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012-2018.
    • The C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012-2018.
  • 51
    • 0034646570 scopus 로고    scopus 로고
    • Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring
    • Usuka,J. and Brendel,V. (2000) Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring. J. Mol. Biol., 297, 1075-1085.
    • (2000) J. Mol. Biol , vol.297 , pp. 1075-1085
    • Usuka, J.1    Brendel, V.2
  • 52
    • 33646493012 scopus 로고    scopus 로고
    • SPA: A probabilistic algorithm for spliced alignment
    • van Nimwegen,E. et al. (2006) SPA: A probabilistic algorithm for spliced alignment. PLoS Genet., 2, e24.
    • (2006) PLoS Genet , vol.2
    • van Nimwegen, E.1
  • 53
    • 33644876253 scopus 로고    scopus 로고
    • Database resources of the national center for biotechnology information
    • Wheeler,D.L. et al. (2006) Database resources of the national center for biotechnology information. Nucleic Acids Res., 34 D173-D180.
    • (2006) Nucleic Acids Res , vol.34
    • Wheeler, D.L.1
  • 54
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: A genomic mapping and alignment program for mRNA and EST sequences
    • Wu,T.D. and Watanabe,C.K. (2005) GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859-1875.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2
  • 55
    • 0035002015 scopus 로고    scopus 로고
    • Computational inference of homologous gene structures in the human genome
    • Yeh,R.F. et al. (2001) Computational inference of homologous gene structures in the human genome. Genome Res., 11, 803-816.
    • (2001) Genome Res , vol.11 , pp. 803-816
    • Yeh, R.F.1
  • 56
    • 0027377256 scopus 로고
    • a weight assay method for splicing signal analysis
    • Zhang,M.Q. and Marr,T.G. (1993) a weight assay method for splicing signal analysis. Comput. Appl. Biosci., 9, 499-509.
    • (1993) Comput. Appl. Biosci , vol.9 , pp. 499-509
    • Zhang, M.Q.1    Marr, T.G.2
  • 57
    • 0141838143 scopus 로고    scopus 로고
    • Spliceosomal introns: New insights into their evolution
    • Zhaxybayeva,O. and Gogarten,J.P. (2003) Spliceosomal introns: New insights into their evolution. Curr. Biol., 13, R764-R766.
    • (2003) Curr. Biol , vol.13
    • Zhaxybayeva, O.1    Gogarten, J.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.