Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
권호 표지

A Genomics Tool for Microbial Genome Comparison Using BLAST/FASTA

BLAST/FASTA를 활용한 미생물 유전체 비교용 도구의 개발

  • Tae, Hongseok (Department of Microbiology, Kyungpook National University) ;
  • Lee, Daesang (Information and Technology Institute, Smallsoft Co., Ltd.) ;
  • Park, Wan (Department of Microbiology, Kyungpook National University) ;
  • Park, Kiejung (Information and Technology Institute, Smallsoft Co., Ltd.)
  • 태홍석 (경북대학교 자연과학대학 미생물학과) ;
  • 이대상 ((주)스몰소프트 정보기술연구소) ;
  • 박완 (경북대학교 자연과학대학 미생물학과) ;
  • 박기정 ((주)스몰소프트 정보기술연구소)
  • Published : 2002.12.01
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Abstract

We have developed GComp as an analysis tool for microbial genome comparison. This tool exploits BLAST or FASTA as a preprocessing program for local alignments to detect homologous regions, parses the homology search results, and generates tables and files to show homology relationship between two genomes at a glance. The interface for graphical representation of the comparative genomic analysis has been also implemented. Our test cases shows that the program can be useful in practice for intuitive and quantitative comparison of microbial genome sequence pairs as well as self-genome analysis. A few additional features have been devised and designed, which will be added in the further development.

미생물 유전체 프로젝트의 결과인 유전체 서열에 대해, 비교 유전체 분석을 수행할 수 있는 분석 도구인 GComp를 개발하였다. 이 도구는 국부 상동성 계산을 BLAST나 FASTA를 사용하여 수행한 후에 그 결과를 받아들여, 상동성을 보이는 부분을 분석하고 위치 파악 및 연결한 뒤, 두 유전체간의 상동성 정도를 일목요연하게 보여줄 수 있는 테이블과 파일들을 생성한다. 한편. 그 결과를 그래픽으로 표시하고 전체를 살펴볼 수 있는 인터페이스 기능을 구현하였다. 시험 데이터로 기존의 미생물 유전체 서열을 상대로 분석하면서, 유전체 서열의 핵산 및 단백질 수준에서의 비교분석 결과를 통해 두 유전체에 대한 비교 정보를 효과적으로 확인할 수 있었고, 보다 다양한 분석을 위한 도구 개발의 기준을 설정할 수 있었다.

Keywords

References

  1. J. Mol. Biol. v.215 Basic local alignment search tool Altschul, S.F.;W. Gish;W. Miller;E.W. Myers;D.J. Lipman
  2. Nucleic Acids Research. v.25 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, S.F.;T.L. Madden;A.A. Schaffer;J. Zhang;Z. Zhang;W. Miller;D.J. Lipman
  3. Math. Modelling and Sci. Computing v.9 Automated pairwise comparisons of microbial genomes Bansal, A.K.;P.Bork;P.J. Stuckey
  4. Bioinformatics v.15 An automated comparative analysis of 17 complete microbial genomes Bansal, A.K.
  5. Nucleic Acids Res. v.30 The Pfam Protein Families Database Bateman A.;E. Birney;L. Cerruti;R. Durbin;L. Etwiller;S.R. Eddy;S.G. Jones;K.L. Howe;M. Marshall;E.L.L. Sonnhammer
  6. Science v.277 The Complete Genome Sequence of Escherichia coli K12 Blattner, F.R.;G. Plunkett;C.A. Bloch;N.T. Perna;V. Burland;M. Riley;J. Collado-Vides;J.D. Glasner;C.K. Rode;G.F. Mayhew;J. Gregor;N.W. Davis;H.A. Kirkpatrick;M.A. Goeden;D.J. Rose;B. Mau;Y. Shao
  7. Nucleic Acids Res. v.27 Alignment of whole genomes Delcher, A.L.;S Kasif;R.D. Fleischmann;J. Peterson;O. White;S.L. Salzberg
  8. Nucleic Acids Res. v.30 Fast algorithms for large-scale genome alignment and comparison Delcher, A.L.;A. Phillippy;J. Carlton;S.L. Salzberg
  9. Science v.269 Whole-genome random sequencing and assembly of Haemophilus influenzae Rd Fleischmann, R.D.;M.D. Adams;O. White;R.A. Clayton;E.F. Kirkness;A.R. Kerlavage;C.J. Bult;J.F. Tomb;B.A. Dougherty;J.M. Merrick
  10. Nucleic Acids Res. v.20 Web-based visualization tools for bacterial genome alignments Folrea, L.;C. Riemer;S. Schwartz;Z. Zhang;N. Stojanovic;W. Miller;M. McClelland
  11. Computer Science and Computational Biology Algorithms on Strings, Trees, and Sequences Gusfield, D.
  12. DNA Res. v.8 Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12 Hayashi, T.;K. Makino;M. Ohnishi;K. Kurokawa;K. Ishii;K. Yokoyama;C.G. Han;E. Ohtsubo;K. Nakayama;T. Murata;M. Tanaka;T. Tobe;T. Iida;G. Takami;T. Honda;C. Sasakawa;N. Ogasawara;T. Yasunaga;S. Kuhara;T. Shiba;M. Hattori;H. Shinagawa
  13. Nature v.406 DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae Heidelberg, J.F.;J.A. Eisen;W.C. Nelson;R.A. Clayton;M.L. Gwinn;R.J. Dodson;D.H. Haft;E.K. Hickey;J.D. Peterson;L. Umayam;S.R. Gill;K.E. Nelson;T.D. Read;H. Tettelin;D. Richardson;M.D. Ermolaeva;J. Vamathevan;S. Bass;H. Qin;I. Dragoi;P. Sellers;L. McDonald;T. Utterback;R.D. Fleishmann;W.C. Nierman;O. White;S.L. Salzberg;H.O. Smith;R.R. Colwell;J.J. Mekalanos;J.C. Venter;C.M. Fraser
  14. Nature v.390 The complete genome sequence of the gram-positive bacterium Bacillus subtilis Kunst, F.;N. Ogasawara;I. Moszer;A.M. Albertini;G. Alloni;V. Azevedo;M.G. Bertero;P. Bessieres;A. Bolotin;S. Borchert;R. Borriss;L. Boursier;A. Brans;M. Braun;S.C Brignell;S. Bron;S. Brouillet;C.V Bruschi;B. Caldwell;V. Capuano;N.M. Carter;S.K. Choi;J.J. Codani;I.F. Connerton;N.J. Cummings;R.A. Daniel;F. Denizot;K.M. Devine;A. Dsuterhoft;S.D. Ehrlich;P.T. Emmerson;K.D. Entian;J. Errington;C. Fabret;E. Ferrari;D. Foulger;C. Fritz;M. Fujita;Y. Fujita;S. Fuma;A. Galizzi;N. Galleron;S.Y. Ghim;P. Glaser;A. Goffeau;E.J. Golightly;G. Grandi;G. Guiseppi;B.J. Guy;K. Haga;J. Haiech;C.R. Harwood;A. Henaut;H. Hilbert;S. Holsappel;S. Hosono;M.F. Hullo;M. Itay
  15. Bioinformatics v.16 VISTA; visualizing global DNA sequence alignments of arbitrary length Mayor, C.;M. Brudno;J.R. Schwartz;A. Poliakov;E.M. Rubin;K.A. Frazer;L.S. Pachter;I. Dubchak
  16. Methods Enzymaol v.183 Rapid and Sensitive Sequence Comparison with FASTP and FASTA Pearson, W.R.
  17. Methods Mol. Biol. v.132 Flexible similarity searching with the FASTA3 program package Pearson, W.R.
  18. Nucleic Acids Res. v.30 Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes Roten, C.H.;P. Gamba;J. Barblan;D. Karamata
  19. Genome Res. v.10 PipMaker. A Web Server for Aligning Two Genomic DNA Sequences Schwartz, S.;Z. Zhang;K.A. Frazer;A. Smit;C. Riemer;J. Bouck;R. Gibbs;R. Hardison;W Miller
  20. Nucleic Acids Res. v.28 Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis Takami, H.;K. Nakasone;Y. Takaki;G. Maeno;R. Sasaki;N. Masui;F. Fuji;C. Hirama;Y. Nakamura;N. Ogasawara;S. Kuhara;K. Horikoshi
  21. Nucleic Acids Res. v.29 The COG database: a tool for genome-scale analysis of protein functions and evolution Tatusov, R.L.;M.Y. Galperin;D.A. Natale;E.V. Koonin
  22. Nucleic Acids Res. v.30 A comparative genomic method for computational identification of prokaryotic translation initiation sites Walker, M.;V. Pavlovic;S. Kasif
  23. Genome Res. v.12 Large-Scale Protein Annotation through Gene Ontology Xie, H.;A. Wasserman;Z. Levine;A. Novik;V. Grebinskiy;A. Shoshan;L Mintz
  24. Science v.298 Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster Zdobnov, E.M.;C. Mering;I. Letunic;D. Torrents;M. Suyama;R.R. Copley;G.K. Christophides;D. Thomasova;R.A. Holt;G.M. Subramanian;H.M. Mueller;G. Dimopoulos;J.H. Law;M.A. Wells;E. Birney;R. Charlab;A.L. Halpern;E. Kokoza;C.L. Kraft;Z. Lai;S. Lewis;C. Louis;C. Barillas-Mury;D. Nusskern;G.M. Rubin;S.L. Salzberg;G.G. Sutton;P. Topalis;R. Wides;P. Wincker;M. Yandell;F.H. Collins;J. Ribeiro;W.M. Gelbart;F.C. Kafatos;P. Bork
  25. Nature v.390 The complete genome sequence of the gram-positive bacterium Bacillus subtilis L. Jones;B. Joris;D. Karamata;Y. Kasahara;M. Klaerr-Blan-chard;C. Klein;Y. Kobayashi;P. Koetter;G. Koningstein;S. Krogh;M. Kumano;K. Kurita;A. Lapidus;S. Lardinois;J. Lauber;V. Lazarevic;S.M. Lee;A. Levine;H. Liu;S. Masuda;C. Mauel;C. Medigue;N. Medina;R.P. Mellado;M. Mizuno;D. Moestl;S. Nakai;M. Noback;D. Noone;M. O'Reilly;K. Ogawa;A. Ogiwara;B. Oudega;S.H. Park;V. Parro;T.M. Pohl;D. Portetelle;S. Porwollik;A.M. Prescott;E. Presecan;P. Pujic;B. Purnelle;G. Rapoport;M. Rey;S. Reynolds;M. Rieger;C. Rivolta;E. Rocha;B. Roche;M. Rose;Y. Sadaie;T. Sato;E. Scanlan;S. Schleich;R. Schroeter;F. Scoffone;J. Sekiguchi;A. Sekowska;S.J. Seror;P. Serror;B.S. Shin;B. Soldo;A. Sorokin;E. Tacconi;T. Takagi;H. Takahashi;K. Takemaru
  26. Nature v.390 The complete genome sequence of the gram-positive bacterium Bacillus subtilis M. Takeuchi;A. Tamakoshi;T. Tanaka;P. Terpstra;A. Tognoni;V.Tosato;S. Uchiyama;M. Vandenbol;F. Vannier;A. Vassarotti;A. Viari;R. Wambutt;E.Wedler;H.Wedler;T.Weitzenegger;P. Winters;A. Wipat;H. Yamamoto;K. Yamane;K. Yasumoto;K. Yata;K. Yoshida;H.F. Yoshikawa;E. Zumstein;H. Yoshikawa;A. Danchin