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A Genomics Tool for Microbial Genome Comparison Using BLAST/FASTA  

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.)
Publication Information
Korean Journal of Microbiology / v.38, no.4, 2002 , pp. 267-275 More about this Journal
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.
Keywords
BLAST; comparative genomics; FASTA; GComp; homology;
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  • Reference
1 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 ] / Science   ScienceOn
2 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 ] / Nucleic Acids Res.   ScienceOn
3 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 ] / Genome Res.   ScienceOn
4 A comparative genomic method for computational identification of prokaryotic translation initiation sites /
[ Walker, M.;V. Pavlovic;S. Kasif ] / Nucleic Acids Res.   ScienceOn
5 An automated comparative analysis of 17 complete microbial genomes /
[ Bansal, A.K. ] / Bioinformatics
6 Basic local alignment search tool /
[ Altschul, S.F.;W. Gish;W. Miller;E.W. Myers;D.J. Lipman ] / J. Mol. Biol.
7 Fast algorithms for large-scale genome alignment and comparison /
[ Delcher, A.L.;A. Phillippy;J. Carlton;S.L. Salzberg ] / Nucleic Acids Res.   ScienceOn
8 Rapid and Sensitive Sequence Comparison with FASTP and FASTA /
[ Pearson, W.R. ] / Methods Enzymaol
9 Alignment of whole genomes /
[ Delcher, A.L.;S Kasif;R.D. Fleischmann;J. Peterson;O. White;S.L. Salzberg ] / Nucleic Acids Res.   ScienceOn
10 Flexible similarity searching with the FASTA3 program package /
[ Pearson, W.R. ] / Methods Mol. Biol.
11 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 ] / Science
12 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 ] / Bioinformatics   ScienceOn
13 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 ] / Nature
14 Web-based visualization tools for bacterial genome alignments /
[ Folrea, L.;C. Riemer;S. Schwartz;Z. Zhang;N. Stojanovic;W. Miller;M. McClelland ] / Nucleic Acids Res.
15 Algorithms on Strings, Trees, and Sequences /
[ Gusfield, D. ] / Computer Science and Computational Biology
16 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 ] / Nucleic Acids Res.   ScienceOn
17 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 ] / Nucleic Acids Res.   ScienceOn
18 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 ] / Nature   ScienceOn
19 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 ] / Nucleic Acids Research.   ScienceOn
20 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 ] / Science
21 Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes /
[ Roten, C.H.;P. Gamba;J. Barblan;D. Karamata ] / Nucleic Acids Res.   ScienceOn
22 Automated pairwise comparisons of microbial genomes /
[ Bansal, A.K.;P.Bork;P.J. Stuckey ] / Math. Modelling and Sci. Computing   ScienceOn
23 Large-Scale Protein Annotation through Gene Ontology /
[ Xie, H.;A. Wasserman;Z. Levine;A. Novik;V. Grebinskiy;A. Shoshan;L Mintz ] / Genome Res.   ScienceOn
24 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 ] / DNA Res.   ScienceOn
25 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 ] / Nature
26 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 ] / Nature