메뉴 건너뛰기




Volumn 10, Issue 4, 2000, Pages 577-586

PipMaker - A web server for aligning two genomic DNA sequences

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; PROTEIN; REPETITIVE DNA;

EID: 0034020416     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.10.4.577     Document Type: Article
Times cited : (1008)

References (39)
  • 3
    • 2642630755 scopus 로고    scopus 로고
    • Analysis of EST-driven gene annotation in human genomic sequence
    • Bailey, L.C., Jr., D.B. Searls, and G.C. Overton. 1998. Analysis of EST-driven gene annotation in human genomic sequence. Genome Res. 8: 362-376.
    • (1998) Genome Res. , vol.8 , pp. 362-376
    • Bailey L.C., Jr.1    Searls, D.B.2    Overton, G.C.3
  • 4
  • 6
    • 0031722856 scopus 로고    scopus 로고
    • Analysis of the quality and utility of random shotgun sequencing at low redundancies
    • Bouck, J., W. Miller, J.H. Gorrell, D. Muzny, and R.A. Gibbs. 1998. Analysis of the quality and utility of random shotgun sequencing at low redundancies. Genome Res. 8: 1074-1084.
    • (1998) Genome Res. , vol.8 , pp. 1074-1084
    • Bouck, J.1    Miller, W.2    Gorrell, J.H.3    Muzny, D.4    Gibbs, R.A.5
  • 7
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge, C. and S. Karlin. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-294.
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-294
    • Burge, C.1    Karlin, S.2
  • 8
    • 0028679375 scopus 로고
    • Recent developments in linear-space alignment methods: A survey
    • Chao, K.-M., R. Hardison, and W. Miller. 1994. Recent developments in linear-space alignment methods: A survey. J. Comput. Biol. 1: 271-291.
    • (1994) J. Comput. Biol. , vol.1 , pp. 271-291
    • Chao, K.-M.1    Hardison, R.2    Miller, W.3
  • 9
    • 0030768930 scopus 로고    scopus 로고
    • Computational methods for the identification of genes in vertebrate genomic sequences
    • Claverie, J.-M. 1997. Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet. 6: 1735-1744.
    • (1997) Hum. Mol. Genet. , vol.6 , pp. 1735-1744
    • Claverie, J.-M.1
  • 11
    • 0343753735 scopus 로고    scopus 로고
    • Cross-species non-coding sequence comparisons identify a coordinate regulator of interleukins 4, 5, and 13
    • in press
    • Cretu, G., R. Locksley, C. Brion, Z.-E. Wang, W. Miller, E.M. Rubin, and K.A. Frazer. 2000. Cross-species non-coding sequence comparisons identify a coordinate regulator of interleukins 4, 5, and 13. Science (in press).
    • (2000) Science
    • Cretu, G.1    Locksley, R.2    Brion, C.3    Wang, Z.-E.4    Miller, W.5    Rubin, E.M.6    Frazer, K.A.7
  • 16
    • 0030076323 scopus 로고    scopus 로고
    • Evolutionary strategies for the elucidation of as and trims factors that regulate the developmental switching programs of the β-like globin genes
    • Gumucio, D., D. Shelton, W. Zhu, D. Millinoff, T. Gray, J. Bock, J. Slightom, and M. Goodman. 1996. Evolutionary strategies for the elucidation of as and trims factors that regulate the developmental switching programs of the β-like globin genes. Mol. Phylog. and Evol. 5: 18-32.
    • (1996) Mol. Phylog. and Evol. , vol.5 , pp. 18-32
    • Gumucio, D.1    Shelton, D.2    Zhu, W.3    Millinoff, D.4    Gray, T.5    Bock, J.6    Slightom, J.7    Goodman, M.8
  • 17
    • 0030722935 scopus 로고    scopus 로고
    • Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome
    • Hardison, R., J. Oeltjen, and W. Miller. 1997a. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res. 7: 959-966.
    • (1997) Genome Res. , vol.7 , pp. 959-966
    • Hardison, R.1    Oeltjen, J.2    Miller, W.3
  • 18
    • 0031593199 scopus 로고    scopus 로고
    • Locus control regions of mammalian β-globin gene clusters: Combining phylogenetic analyses and experimental results to gain functional insights
    • Hardison, R., J.L. Slightom, D.L. Gumucio, M. Goodman, N. Stojanovic, and W. Miller. 1997b. Locus control regions of mammalian β-globin gene clusters: Combining phylogenetic analyses and experimental results to gain functional insights. Gene 205: 73-94.
    • (1997) Gene , vol.205 , pp. 73-94
    • Hardison, R.1    Slightom, J.L.2    Gumucio, D.L.3    Goodman, M.4    Stojanovic, N.5    Miller, W.6
  • 19
    • 0032564409 scopus 로고    scopus 로고
    • Nitrosative stress: Metabolic pathway involving the flavohemoglobin
    • Hausladen, A., A.J. Gow, and J.S. Stamler. 1998. Nitrosative stress: Metabolic pathway involving the flavohemoglobin. Proc. Natl. Acad. Sci. 95: 14100-14105.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 14100-14105
    • Hausladen, A.1    Gow, A.J.2    Stamler, J.S.3
  • 20
    • 0029669270 scopus 로고    scopus 로고
    • Continental breakup and the ordinal diversification of birds and mammals
    • Hedges, S.B., P.H. Parker, C.G. Sibley, and S. Kumar. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381: 226-229.
    • (1996) Nature , vol.381 , pp. 226-229
    • Hedges, S.B.1    Parker, P.H.2    Sibley, C.G.3    Kumar, S.4
  • 21
    • 0033012366 scopus 로고    scopus 로고
    • Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13
    • Jang, W., A. Hua, S.V. Spilson, W. Miller, B.A. Roe, and M.H. Meisler. 1999. Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13. Genome Res. 9: 53-61.
    • (1999) Genome Res. , vol.9 , pp. 53-61
    • Jang, W.1    Hua, A.2    Spilson, S.V.3    Miller, W.4    Roe, B.A.5    Meisler, M.H.6
  • 22
    • 0029164978 scopus 로고
    • Human and rodent sequence comparisons: A mosaic model of genomic evolution
    • Koop, B.F. 1995. Human and rodent sequence comparisons: A mosaic model of genomic evolution. Trends Genet. 11: 367-371.
    • (1995) Trends Genet. , vol.11 , pp. 367-371
    • Koop, B.F.1
  • 23
    • 0027963488 scopus 로고
    • Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA
    • Koop, B.F. and L. Hood. 1994. Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nat. Genet. 7: 48-53.
    • (1994) Nat. Genet. , vol.7 , pp. 48-53
    • Koop, B.F.1    Hood, L.2
  • 24
    • 0029805706 scopus 로고    scopus 로고
    • The new genomics: Global views of biology
    • Lander, E.S. 1996. The new genomics: Global views of biology. Science 274: 536-539.
    • (1996) Science , vol.274 , pp. 536-539
    • Lander, E.S.1
  • 25
    • 0030076124 scopus 로고    scopus 로고
    • Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis
    • Li, W., D. Ellsworth, J. Krushkal, B. Chang, and D. Hewett-Emmett. 1996. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol. 5: 182-187.
    • (1996) Mol. Phylogenet. Evol. , vol.5 , pp. 182-187
    • Li, W.1    Ellsworth, D.2    Krushkal, J.3    Chang, B.4    Hewett-Emmett, D.5
  • 26
    • 0032729835 scopus 로고    scopus 로고
    • Structure and expression of the human and mouse novel unconventional myosin XV genes responsible tor hereditary deafness, DFNB3 and shaker-2
    • Liang, Y., A. Wang, I. Belyantseva, D. Anderson, F.J. Probst, T.D. Barber, W. Miller, J. Touchman, L. Jin, S. Sullivan et al. 1999. Structure and expression of the human and mouse novel unconventional myosin XV genes responsible tor hereditary deafness, DFNB3 and shaker-2. Genomics 61: 243-258.
    • (1999) Genomics , vol.61 , pp. 243-258
    • Liang, Y.1    Wang, A.2    Belyantseva, I.3    Anderson, D.4    Probst, F.J.5    Barber, T.D.6    Miller, W.7    Touchman, J.8    Jin, L.9    Sullivan, S.10
  • 27
    • 0029901632 scopus 로고    scopus 로고
    • RNA polymerase, PurR and MetR interactions at the glyA promoter of Escherichia coli
    • Lorenz, E. and G.V. Stauffer. 1996. RNA polymerase, PurR and MetR interactions at the glyA promoter of Escherichia coli. Microbiology 142: 1819-1824.
    • (1996) Microbiology , vol.142 , pp. 1819-1824
    • Lorenz, E.1    Stauffer, G.V.2
  • 28
    • 0032483028 scopus 로고    scopus 로고
    • Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences
    • Makalowski, W. and M.S. Boguski. 1998. Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. 95: 9407-9412.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 9407-9412
    • Makalowski, W.1    Boguski, M.S.2
  • 29
    • 0033612071 scopus 로고    scopus 로고
    • Human Genome Project. Sequencers endorse plan for a draft in 1 year
    • Marshall, E. 1999. Human Genome Project. Sequencers endorse plan for a draft in 1 year. Science 284: 1439-1441.
    • (1999) Science , vol.284 , pp. 1439-1441
    • Marshall, E.1
  • 30
    • 0031669416 scopus 로고    scopus 로고
    • Comparison of sample sequences of the Salmonella typhi genome to the sequence of the complete Escherichia coli K-12 genome
    • McClelland, M. and R.K. Wilson. 1998. Comparison of sample sequences of the Salmonella typhi genome to the sequence of the complete Escherichia coli K-12 genome. Infect. Immun. 66: 4305-4312.
    • (1998) Infect. Immun. , vol.66 , pp. 4305-4312
    • McClelland, M.1    Wilson, R.K.2
  • 31
    • 0031844664 scopus 로고    scopus 로고
    • A novel mechanism for upregulation of the Escherichia coli K-12 hmp (flavohemoglobin) gene by the "NO releaser," S-nitrosoglutathione: Nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region
    • Membrillo-Hernandez, J., M.D. Coopamah, A. Channa, M.N. Hughes, and R.K. Poole. 1998. A novel mechanism for upregulation of the Escherichia coli K-12 hmp (flavohemoglobin) gene by the "NO releaser," S-nitrosoglutathione: Nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region. Mol. Microbiol. 29: 1101-1112.
    • (1998) Mol. Microbiol. , vol.29 , pp. 1101-1112
    • Membrillo-Hernandez, J.1    Coopamah, M.D.2    Channa, A.3    Hughes, M.N.4    Poole, R.K.5
  • 32
    • 0032173633 scopus 로고    scopus 로고
    • Rates and patterns of chromosome evolution in enteric bacteria
    • Ochman, H. and U. Bergthorsson. 1998. Rates and patterns of chromosome evolution in enteric bacteria. Curr. Opin. Microbiol. 1: 580-583.
    • (1998) Curr. Opin. Microbiol. , vol.1 , pp. 580-583
    • Ochman, H.1    Bergthorsson, U.2
  • 33
    • 0028697888 scopus 로고
    • The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium
    • Ochman, H. and E.A. Groisman. 1994. The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium. Exs 69: 479-493.
    • (1994) Exs , vol.69 , pp. 479-493
    • Ochman, H.1    Groisman, E.A.2
  • 34
    • 0030966052 scopus 로고    scopus 로고
    • Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains
    • Oeltjen, J.C., T.M. Malley, D.M. Muzny, W. Miller, R.A. Gibbs, and J.W. Belmont. 1997. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res. 7: 315-329.
    • (1997) Genome Res. , vol.7 , pp. 315-329
    • Oeltjen, J.C.1    Malley, T.M.2    Muzny, D.M.3    Miller, W.4    Gibbs, R.A.5    Belmont, J.W.6
  • 35
  • 36
    • 0032923247 scopus 로고    scopus 로고
    • Functional genomics in Caenorhabditis elegans: An approach involving comparisons of sequences from related nematodes
    • Thacker, C., M.A. Marra, A. Jones, D.L. Baillie, and A.M. Rose. 1999. Functional genomics in Caenorhabditis elegans: An approach involving comparisons of sequences from related nematodes. Genome Res. 9: 348-359.
    • (1999) Genome Res. , vol.9 , pp. 348-359
    • Thacker, C.1    Marra, M.A.2    Jones, A.3    Baillie, D.L.4    Rose, A.M.5
  • 37
    • 0033046314 scopus 로고    scopus 로고
    • Sample sequencing of a Salmonella typhimurium LT2 lambda library: Comparison to the Escherichia coli K12 genome
    • Wong, R.M., K.K. Wong, N.R. Benson, and M. McClelland. 1999. Sample sequencing of a Salmonella typhimurium LT2 lambda library: Comparison to the Escherichia coli K12 genome. FEMS Microbiol. Lett. 173: 411-423.
    • (1999) FEMS Microbiol. Lett. , vol.173 , pp. 411-423
    • Wong, R.M.1    Wong, K.K.2    Benson, N.R.3    McClelland, M.4
  • 38
    • 0031927028 scopus 로고    scopus 로고
    • Alignments without low-scoring regions
    • Zhang, Z., P. Berman, and W. Miller. 1998. Alignments without low-scoring regions. J. Comput. Biol. 5: 197-210.
    • (1998) J. Comput. Biol. , vol.5 , pp. 197-210
    • Zhang, Z.1    Berman, P.2    Miller, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.