Data integration in microbial genomics ... - Jacobs University

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76 5. Megx.net NCBI Genome 5.5 Summary Since its first publication [Lombardot et al., 2006], megx.net has undergone extensive development. The web design has been revamped for better user experience, and the database content greatly enhanced, providing considerably more genomes and metagenomes, marine phages and rRNA sequence data. Megx.net’s unique integration of environmental and sequence data allows microbial ecologists and marine scientists to better contextualize and compare biological data, using, e.g. the Genes Mapserver and GIS Tools. The integrated datasets facilitate a holistic approach to understanding the complex interplay between organisms, genes and their environment. As such, megx.net serves as a fundamental resource in the emerging field of ecosystem biology, and paves the road to a better understanding of the complex responses and adaptations of organisms to environmental change. Database access The database and all described resources are freely available at http: //www.megx.net/. Continuously updated statistics of the content are available at http://www.megx.net/content. A web feed for news related to megx.net is available at http://www.megx.net/portal/news/. Feedback and comments, the most effective springboard for further improvements, are welcome at http://www.megx.net/portal/contact.html and via email to megx@mpi-bremen.de. Overall, it is important to note that the megx.net website does not fully reflect the content and search functionalities of MegDB. For any specialized data request, contact the corresponding author. Funding FP6 EU project MetaFunctions (CT 511784); Network of Excellence ‘Marine Genomics Europe’; Max Planck Society. Funding for open
5.5. Summary 77 access charge: Max Planck Society. Conflict of interest statement. None declared. Acknowledgements We would like to acknowledge Timmy Schweer, Thierry Lombardot, Magdalena Golden and Laura Sandrine for their valuable input to megx.net, as well as David E. Todd for redesigning the web page.
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Max Planck Institute for Marine Mic
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List of abbreviations BLAST Basic L
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Thesis abstract Deoxyribonucleic ac
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4.2 Introduction . . . . . . . . .
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2 1. Introduction syntax: data leve
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4 1. Introduction used to derive ne
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6 1. Introduction croorganisms thri
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8 1. Introduction the middle at the
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10 1. Introduction marker genes hel
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12 1. Introduction what kind and wh
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14 1. Introduction possibilities li
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16 1. Introduction tual data acquis
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18 1. Introduction Doug Wendel, Owe
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CHAPTER 2 METABAR A tool for consis
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2.2. Background 23 molecular sequen
Page 33 and 34: 2.2. Background 25 printing of data
Page 35 and 36: 2.4. Results 27 KML export function
Page 37 and 38: 2.4. Results 29 Figure 2.3: Screens
Page 39 and 40: 2.5. Discussion 31 taking samples i
Page 41 and 42: 2.5. Discussion 33 Handlebar MetaBa
Page 43 and 44: 2.6. Conclusion 35 rine Microbiolog
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Page 48 and 49: 40 3. CDinFusion Genomic Standards
Page 50 and 51: 42 3. CDinFusion sortium (GSC), an
Page 52 and 53: 44 3. CDinFusion tiFASTA file with
Page 54 and 55: 46 3. CDinFusion offered the option
Page 56 and 57: 48 3. CDinFusion AMD Opteron TM pro
Page 58 and 59: 50 3. CDinFusion able separately an
Page 60 and 61: 52 3. CDinFusion and upload it with
Page 63 and 64: CHAPTER 4 MIMARKS The Minimum infor
Page 65 and 66: 4.2. Introduction 57 edge generatio
Page 67 and 68: 4.3. Development of MIMARKS 59 in t
Page 69 and 70: 4.4. Survey of published parameters
Page 71 and 72: 4.5. The MIMARKS checklist 63 Resul
Page 73 and 74: 4.6. Conclusions and call for actio
Page 75 and 76: CHAPTER 5 MEGX.NET Integrated datab
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Page 81 and 82: 5.4. User Access 73 5.4 User Access
Page 83: 5.4. User Access 75 tal context, co
Page 88 and 89: 80 6. Domains of unknown function 6
Page 90 and 91: 82 6. Domains of unknown function F
Page 92 and 93: 84 6. Domains of unknown function p
Page 95 and 96: CHAPTER 7 SUMMARY AND DISCUSSION Th
Page 97 and 98: 7.2. GSC standards development 89 T
Page 99 and 100: 7.2. GSC standards development 91 o
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Page 106 and 107: 98 8. Conclusion and outlook nities
Page 108 and 109: 100 8. Conclusion and outlook plina
Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
Page 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
Page 114 and 115: 106 BIBLIOGRAPHY [Giovannoni et al.
Page 116 and 117: 108 BIBLIOGRAPHY [Kitano, 2002] Kit
Page 118 and 119: 110 BIBLIOGRAPHY pathways in marine
Page 120 and 121: 112 BIBLIOGRAPHY [Ramette, 2007] Ra
Page 122 and 123: 114 BIBLIOGRAPHY (2006). Microbial
Page 124 and 125: 116 BIBLIOGRAPHY [Williamson et al.
Page 127: CHAPTER 9 ACKNOWLEDGEMENTS First, I
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