메뉴 건너뛰기




Volumn 9, Issue , 2008, Pages

CoCoNUT: An efficient system for the comparison and analysis of genomes

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMICS; COMPARISON AND ANALYSIS; GENOME COMPARISON; INTERACTIVE VISUALIZATIONS; LARGE GENOMIC SEQUENCES; LARGE-SCALE STUDIES; SEGMENTAL DUPLICATIONS; STATE-OF-THE-ART ALGORITHMS;

EID: 65349107123     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-476     Document Type: Article
Times cited : (25)

References (47)
  • 1
    • 0142056169 scopus 로고    scopus 로고
    • An Applications-Focused Review of Comparative Genomics Tools: Capabilities, Limitations and Future Challenges
    • 12846393
    • Chain P Kurtz S Ohlebusch E Slezak T An Applications-Focused Review of Comparative Genomics Tools: Capabilities, Limitations and Future Challenges Briefings in Bioinformatics 2003, 4(2):105-123. 12846393
    • (2003) Briefings in Bioinformatics , vol.4 , Issue.2 , pp. 105-123
    • Chain, P.1    Kurtz, S.2    Ohlebusch, E.3    Slezak, T.4
  • 2
    • 33750441484 scopus 로고    scopus 로고
    • M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species
    • 1629028 17022809
    • Treangen T Messeguer X M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species BMC Bioinformatics 2006, 7:433. 1629028 17022809
    • (2006) BMC Bioinformatics , vol.7 , pp. 433
    • Treangen, T.1    Messeguer, X.2
  • 4
  • 5
    • 43449126511 scopus 로고    scopus 로고
    • Space efficient computation of rare maximal exact matches between multiple sequences
    • 18361760
    • Ohlebusch E Kurtz S Space efficient computation of rare maximal exact matches between multiple sequences J Comput Biol 2008, 15(4):357-377. 18361760
    • (2008) J Comput Biol , vol.15 , Issue.4 , pp. 357-377
    • Ohlebusch, E.1    Kurtz, S.2
  • 6
    • 18544380734 scopus 로고    scopus 로고
    • A Local Chaining Algorithm and its Applications in Comparative Genomics
    • LNBI 2812, Springer Verlag
    • Abouelhoda M Ohlebusch E A Local Chaining Algorithm and its Applications in Comparative Genomics Proc. 3rd Workshop on Algorithms in Bioinformatics LNBI 2812, Springer Verlag 2003, 1-16.
    • (2003) Proc. 3rd Workshop on Algorithms in Bioinformatics , pp. 1-16
    • Abouelhoda, M.1    Ohlebusch, E.2
  • 7
    • 18544371168 scopus 로고    scopus 로고
    • Chaining Algorithms and applications in comparative genomics
    • Abouelhoda M Ohlebusch E Chaining Algorithms and applications in comparative genomics J Discrete Algorithms 2005, 3(2-4):321-341.
    • (2005) J Discrete Algorithms , vol.3 , Issue.2-4 , pp. 321-341
    • Abouelhoda, M.1    Ohlebusch, E.2
  • 8
    • 38049009061 scopus 로고    scopus 로고
    • A Chaining Algorithm for Mapping cDNA Sequences to Multiple Genomic Sequences
    • Lecture Notes in Computer Science 4726, Springer Verlag
    • Abouelhoda M A Chaining Algorithm for Mapping cDNA Sequences to Multiple Genomic Sequences Proc. 14th International Symposium on String Processing and Information Retrieval Lecture Notes in Computer Science 4726, Springer Verlag 2007, 1-13.
    • (2007) Proc. 14th International Symposium on String Processing and Information Retrieval , pp. 1-13
    • Abouelhoda, M.1
  • 9
    • 0029654258 scopus 로고
    • A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis
    • 8566757
    • Sonnhammer E Durbin R A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis Gene 1995, 167:GC1-GC10. 8566757
    • (1995) Gene , vol.167
    • Sonnhammer, E.1    Durbin, R.2
  • 10
    • 34249734822 scopus 로고    scopus 로고
    • Gepard: A rapid and sensitive tool for creating dotplots on genome scale
    • 17309896
    • Krumsiek J Arnold R Rattei T Gepard: A rapid and sensitive tool for creating dotplots on genome scale Bioinformatics 2007, 23(8):1026-1028. 17309896
    • (2007) Bioinformatics , vol.23 , Issue.8 , pp. 1026-1028
    • Krumsiek, J.1    Arnold, R.2    Rattei, T.3
  • 11
    • 8744312854 scopus 로고    scopus 로고
    • A novel method for multiple alignment of sequences with repeated and shuffled elements
    • 525693 15520295
    • Raphael B Zhi D Tang H Pevzner P A novel method for multiple alignment of sequences with repeated and shuffled elements Genome Research 2004, 14(11):2336-2346. 525693 15520295
    • (2004) Genome Research , vol.14 , Issue.11 , pp. 2336-2346
    • Raphael, B.1    Zhi, D.2    Tang, H.3    Pevzner, P.4
  • 12
  • 14
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangement
    • 442156 15231754
    • Darling A Mau B Blattner F Perna N Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangement Genome Research 2004, 14:1394-1403. 442156 15231754
    • (2004) Genome Research , vol.14 , pp. 1394-1403
    • Darling, A.1    Mau, B.2    Blattner, F.3    Perna, N.4
  • 16
    • 26444609698 scopus 로고    scopus 로고
    • Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes
    • LNBI 3388, Springer-Verlag
    • Mau B Darling A Perna N Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes Proc. Workshop on Comparative Genomics LNBI 3388, Springer-Verlag 2005, 72-84.
    • (2005) Proc. Workshop on Comparative Genomics , pp. 72-84
    • Mau, B.1    Darling, A.2    Perna, N.3
  • 18
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-Like Alignment Tool
    • 187518 11932250
    • Kent W BLAT - The BLAST-Like Alignment Tool Genome Research 2002, 12:656-664. 187518 11932250
    • (2002) Genome Research , vol.12 , pp. 656-664
    • Kent, W.1
  • 20
    • 28844465123 scopus 로고    scopus 로고
    • Engineering a software tool for gene structure prediction in higher organisms
    • Gremme G Brendel V Sparks M Kurtz S Engineering a software tool for gene structure prediction in higher organisms Information and Software Technology 2005, 47(15):965-978.
    • (2005) Information and Software Technology , vol.47 , Issue.15 , pp. 965-978
    • Gremme, G.1    Brendel, V.2    Sparks, M.3    Kurtz, S.4
  • 21
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
    • 15728110
    • Wu T Watanabe C GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences Bioinformatics 2005, 21(9):1859-1875. 15728110
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1859-1875
    • Wu, T.1    Watanabe, C.2
  • 23
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: Finding Local Similarities by Multiple Sequence Alignment
    • 9614273
    • Morgenstern B Frech K Dress A Werner T DIALIGN: Finding Local Similarities by Multiple Sequence Alignment Bioinformatics 1998, 14:290-294. 9614273
    • (1998) Bioinformatics , vol.14 , pp. 290-294
    • Morgenstern, B.1    Frech, K.2    Dress, A.3    Werner, T.4
  • 24
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • 430158 12654723
    • Brudno M Do C Cooper G Kim M Davydov E NISC Comparative Sequencing Program Green E Sidow A Batzoglou S LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA Genome Research 2003, 13(4):721-731. 430158 12654723
    • (2003) Genome Research , vol.13 , Issue.4 , pp. 721-731
    • Brudno, M.1    Do, C.2    Cooper, G.3    Kim, M.4    Davydov, E.5    Green, E.6    Sidow, A.7    Batzoglou, S.8
  • 26
    • 0036202921 scopus 로고    scopus 로고
    • PatternHunter: Faster and More Sensitive Homology Search
    • 11934743
    • Ma B Tromp J Li M PatternHunter: Faster and More Sensitive Homology Search Bioinformatics 2002, 18(3):440-445. 11934743
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 440-445
    • Ma, B.1    Tromp, J.2    Li, M.3
  • 31
  • 32
    • 0038673215 scopus 로고
    • Patterns in DNA and amino acid sequences and their statistical significance
    • CRC Press
    • Karlin S Ost F Blaisdell B Patterns in DNA and amino acid sequences and their statistical significance Mathematical Methods for DNA Sequences CRC Press 1989, 133-157.
    • (1989) Mathematical Methods for DNA Sequences , pp. 133-157
    • Karlin, S.1    Ost, F.2    Blaisdell, B.3
  • 33
    • 0027968068 scopus 로고
    • CLUSTALW: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position Specific Gap Penalties, and Weight Matrix Choice
    • 308517 7984417
    • Thompson J Higgins D Gibson T CLUSTALW: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position Specific Gap Penalties, and Weight Matrix Choice Nucleic Acids Research 1994, 22:4673-4680. 308517 7984417
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.1    Higgins, D.2    Gibson, T.3
  • 37
    • 1842768393 scopus 로고    scopus 로고
    • Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes
    • 383294 15059991
    • Bourque G Pevzner P Tesler G Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes Genome Research 2004, 14:507-516. 383294 15059991
    • (2004) Genome Research , vol.14 , pp. 507-516
    • Bourque, G.1    Pevzner, P.2    Tesler, G.3
  • 38
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 12748633
    • Kellis M Patterson N Endrizzi M Birren B Lander E Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003, 423:241-254. 12748633
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.5
  • 41
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative 11130711
    • The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 2000, 408:796-815. 11130711
    • (2000) Nature , vol.408 , pp. 796-815
  • 42
    • 0034671866 scopus 로고    scopus 로고
    • The Origins of Genomic Duplications in Arabidopsis
    • 11118139
    • Vision T Brown D Tanksley S The Origins of Genomic Duplications in Arabidopsis Science 2000, 290:2114-2117. 11118139
    • (2000) Science , vol.290 , pp. 2114-2117
    • Vision, T.1    Brown, D.2    Tanksley, S.3
  • 43
    • 0031732094 scopus 로고    scopus 로고
    • A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence
    • 310774 9750195
    • Florea L Hartzell G Zhang Z Rubin G Miller W A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence Genome Research 1998, 8:967-974. 310774 9750195
    • (1998) Genome Research , vol.8 , pp. 967-974
    • Florea, L.1    Hartzell, G.2    Zhang, Z.3    Rubin, G.4    Miller, W.5
  • 44
    • 0021760028 scopus 로고
    • Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes
    • 321070 6364041
    • Staden R Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes Nucleic Acids Res 1984, 12(1 Pt 2):551-567. 321070 6364041
    • (1984) Nucleic Acids Res , vol.12 , Issue.1 PART 2 , pp. 551-567
    • Staden, R.1
  • 46
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • 17055251
    • Bentley DR Whole-genome re-sequencing Curr Opin Genet Dev 2006, 16(6):545-52. 17055251
    • (2006) Curr Opin Genet Dev , vol.16 , Issue.6 , pp. 545-552
    • Bentley, D.R.1
  • 47
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • 18262675
    • Mardis E The impact of next-generation sequencing technology on genetics Trends Genet 2008, 24(3):133-41. 18262675
    • (2008) Trends Genet , vol.24 , pp. 133-141
    • Mardis, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.