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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: [email protected].
    • 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 P 1998 Conservation of gene order: a fingerprint of proteins that physically interact Trends Biochem Sci 23 324 328 10.1016/S0968-0004(98)01274-2 9787636 http://dx.doi.org/10.1016/S0968-0004(98)01274-2
2. Marcotte EM, Pellegrini M, Ho-Leung N, Rice D, Yeates T, Eisenberg D 1999 Detecting protein function and protein-protein interactions from genome sequences Science 285 751 753 10.1126/science.285.5428.751 10427000 http://dx.doi.org/10.1126/science.285.5428.751
3. Overbeek R, Fonstein M, D’Souza M, Pusch GD, Maltsev N 1999 The use of gene clusters to infer functional coupling Proc Natl Acad Sci USA 96 2896 2901 10.1073/pnas.96.6.2896 10077608 http://dx.doi.org/10.1073/pnas.96.6.2896
4. Owston RD 1997 The world wide web: a technology to enhance teaching and learning? Educ Researcher 26 27 33
5. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO 1999 Assigning protein functions by comparative genome analysis: protein phylogenetic profiles Proc Natl Acad Sci USA 96 4285 4288 10.1073/pnas.96.8.4285 10200254 http://dx.doi.org/10.1073/pnas.96.8.4285
6. Salgado H, Moreno-Haelsieb G, Smith T, Collado-Vides J 2000 Operons in Escherichia coli: genomic analysis and predictions Proc Natl Acad Sci USA 97 6652 6657 10.1073/pnas.110147297 10823905 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 J 2001 RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12 Nucleic Acids Res 29 72 74 10.1093/nar/29.1.72 29794 http://dx.doi.org/10.1093/nar/29.1.72
8. Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D 2003 Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach Genome Biol 4 R59 10.1186/gb-2003-4-9-r59 12952538 193659 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 D 2003 Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps Nucleic Acids Res 31 7099 7109 10.1093/nar/gkg924 14654685 291866 http://dx.doi.org/10.1093/nar/gkg924
10. Tuckman BW 2002 Evaluating ADAPT: a hybrid instructional model combining web-based and classroom components Computers Educ 39 261 269 10.1016/S0360-1315(02)00045-3 http://dx.doi.org/10.1016/S0360-1315(02)00045-3
11. Tzvetkov M, Klopprogge C, Zelder O, Liebl W 2003 Genetic dissection of trehalose biosynthesis in Corynebacterium glutamicum: inactivation of trehalose production leads to impaired growth and an altered cell wall lipid composition Microbiology 149 1659 1673 10.1099/mic.0.26205-0 12855718 http://dx.doi.org/10.1099/mic.0.26205-0
12. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B 2003 STRING: a database of predicted functional associations between proteins Nucleic Acids Res 31 258 261 10.1093/nar/gkg034 12519996 165481 http://dx.doi.org/10.1093/nar/gkg034
13. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D 2002 DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions Nucleic Acids Res 30 303 305 10.1093/nar/30.1.303 99070 http://dx.doi.org/10.1093/nar/30.1.303

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/content/journal/jmbe/10.1128/jmbe.v5.71
2004-05-01
2019-10-20

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
Download as Powerpoint

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