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A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes

    Authors: MICHAEL STRONG1,*, DUILIO CASCIO1, DAVID EISENBERG1
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    Affiliations: 1: Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Box 951570, Los Angeles, California 90095-1570
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • *Corresponding author. Mailing address: Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Box 951570, Los Angeles, CA 90095-1570. Phone: 310-206-3642. Fax: 310-206-3914. E-mail: strong@mbi.ucla.edu.
    • Copyright © 2004, American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 30-35. doi:10.1128/jmbe.v5.71
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    Abstract:

    As the number of completely sequenced microbial genomes continues to rise at an impressive rate, it is important to prepare students with the skills necessary to investigate microorganisms at the genomic level. As a part of the core curriculum for first-year graduate students in the biological sciences, we have implemented a web-based tutorial to introduce students to the fields of comparative and functional genomics. The tutorial focuses on recent computational methods for identifying functionally linked genes and proteins on a genome-wide scale and was used to introduce students to the Rosetta Stone, Phylogenetic Profile, conserved Gene Neighbor, and Operon computational methods. Students learned to use a number of publicly available web servers and databases to identify functionally linked genes in the genome, with emphasis on genome organization and operon structure. The overall effectiveness of the tutorial was assessed based on student evaluations and homework assignments. The tutorial is available to other educators at http://www.doe-mbi.ucla.edu/~strong/m253.php.

Key Concept Ranking

Pyrobaculum aerophilum
0.51
Escherichia coli
0.4962061
Fusion Gene
0.44790193
0.51

References & Citations

1. Dandekar T, Snel B, Huynen M, Bork P1998Conservation of gene order: a fingerprint of proteins that physically interactTrends Biochem Sci2332432810.1016/S0968-0004(98)01274-29787636 http://dx.doi.org/10.1016/S0968-0004(98)01274-2
2. Marcotte EM, Pellegrini M, Ho-Leung N, Rice D, Yeates T, Eisenberg D1999Detecting protein function and protein-protein interactions from genome sequencesScience28575175310.1126/science.285.5428.75110427000 http://dx.doi.org/10.1126/science.285.5428.751
3. Overbeek R, Fonstein M, D’Souza M, Pusch GD, Maltsev N1999The use of gene clusters to infer functional couplingProc Natl Acad Sci USA962896290110.1073/pnas.96.6.289610077608 http://dx.doi.org/10.1073/pnas.96.6.2896
4. Owston RD1997The world wide web: a technology to enhance teaching and learning?Educ Researcher262733
5. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO1999Assigning protein functions by comparative genome analysis: protein phylogenetic profilesProc Natl Acad Sci USA964285428810.1073/pnas.96.8.428510200254 http://dx.doi.org/10.1073/pnas.96.8.4285
6. Salgado H, Moreno-Haelsieb G, Smith T, Collado-Vides J2000Operons in Escherichia coli: genomic analysis and predictionsProc Natl Acad Sci USA976652665710.1073/pnas.11014729710823905 http://dx.doi.org/10.1073/pnas.110147297
7. Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Diaz-Peredo E, Sanchez-Solano F, Perez-Rueda E, Bonavides-Martinez C, Collado-Vides J2001RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12Nucleic Acids Res29727410.1093/nar/29.1.7229794 http://dx.doi.org/10.1093/nar/29.1.72
8. Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D2003Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approachGenome Biol4R5910.1186/gb-2003-4-9-r5912952538193659 http://dx.doi.org/10.1186/gb-2003-4-9-r59
9. Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D2003Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage mapsNucleic Acids Res317099710910.1093/nar/gkg92414654685291866 http://dx.doi.org/10.1093/nar/gkg924
10. Tuckman BW2002Evaluating ADAPT: a hybrid instructional model combining web-based and classroom componentsComputers Educ3926126910.1016/S0360-1315(02)00045-3 http://dx.doi.org/10.1016/S0360-1315(02)00045-3
11. Tzvetkov M, Klopprogge C, Zelder O, Liebl W2003Genetic dissection of trehalose biosynthesis in Corynebacterium glutamicum: inactivation of trehalose production leads to impaired growth and an altered cell wall lipid compositionMicrobiology1491659167310.1099/mic.0.26205-012855718 http://dx.doi.org/10.1099/mic.0.26205-0
12. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B2003STRING: a database of predicted functional associations between proteinsNucleic Acids Res3125826110.1093/nar/gkg03412519996165481 http://dx.doi.org/10.1093/nar/gkg034
13. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D2002DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactionsNucleic Acids Res3030330510.1093/nar/30.1.30399070 http://dx.doi.org/10.1093/nar/30.1.303
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2004-05-01
2017-11-18

Abstract:

As the number of completely sequenced microbial genomes continues to rise at an impressive rate, it is important to prepare students with the skills necessary to investigate microorganisms at the genomic level. As a part of the core curriculum for first-year graduate students in the biological sciences, we have implemented a web-based tutorial to introduce students to the fields of comparative and functional genomics. The tutorial focuses on recent computational methods for identifying functionally linked genes and proteins on a genome-wide scale and was used to introduce students to the Rosetta Stone, Phylogenetic Profile, conserved Gene Neighbor, and Operon computational methods. Students learned to use a number of publicly available web servers and databases to identify functionally linked genes in the genome, with emphasis on genome organization and operon structure. The overall effectiveness of the tutorial was assessed based on student evaluations and homework assignments. The tutorial is available to other educators at http://www.doe-mbi.ucla.edu/~strong/m253.php.

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FIG. 1

Introductory page for the web-based comparative genomics tutorial. This tutorial is available at http://www.doembi.ucla.edu/~strong/m253.php.

Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 30-35. doi:10.1128/jmbe.v5.71
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FIG. 2

Overview of the four databases and web servers used in the web-based tutorial: European Molecular Biology Laboratory Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Pasteur Institute GenoList, RegulonDB, and Database of Interacting Proteins.

Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 30-35. doi:10.1128/jmbe.v5.71
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FIG. 3

Summary of functional linkages involving the gene, which is involved in the first step of trehalose biosynthesis. This gene is linked to , which is involved in the second step of trehalose biosynthesis, by the conserved Gene Neighbor, Phylogenetic Profile, Rosetta Stone, and Operon computational methods.

Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 30-35. doi:10.1128/jmbe.v5.71
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Image of FIG. 4

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FIG. 4

Functional genomics homework problem set.

Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 30-35. doi:10.1128/jmbe.v5.71
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