Data integration in microbial genomics ... - Jacobs University

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74 5. Megx.net such as temperature, dissolved oxygen, nitrate and chlorophyll concentrations, over specified monthly, seasonally or annually intervals (Figure 5.2f). Geographic-BLAST The Geographic-BLAST tool queries the MegDB genome, metagenome, marine phages and rRNA sequence data using the BLAST algorithm [Altschul et al., 1990]. The results are reported according to the sample locations (when provided) of the database hits. With the updated Geographic-BLAST, results are plotted on the Genes Mapserver world map, where they are labeled by number of hits per site (Figure 5.2). Standard BLAST results are shown in a table, which also provides direct access to the associated contextual data of the hits. Software extensions to the portal In addition to the services directly provided by megx.net, the project serves as a portal to software for general data analysis in microbial genomics. MetaBar (http://www.megx.net/metabar) is a tool developed with the aim to help investigators efficiently capture, store and submit contextual data gathered in the field. It is designed to support the complete workflow from the sampling event up to the metadata-enriched sequence submission to an INSDC database. MicHanThi (http://www.megx.net/michanthi) is a software tool designed to facilitate the genome annotation process through rapid, high-quality prediction of gene functions. It clearly out-performs the human annotator in terms of accuracy and reproducibility. JCoast (http://www.megx.net/jcoast; [Richter, 2003]) is a desktop application primarily designed to analyze and compare (meta)genome sequences of prokaryotes. JCoast offers a flexible graphical user interface, as well as an application programming interface that facilitates back-end data access to GenDB projects [Meyer et al., 2003]. JCoast offers individual, cross genome and metagenome analysis, including access to Geographic-BLAST. User test case To demonstrate the interpretation of genomic content in environmen-
5.4. User Access 75 tal context, consider a test case with the marine phages. Marine phage genomes [Sullivan et al., 2005] and ‘viral’ classified GOS scaffolds [Williamson et al., 2008] have revealed host-related metabolic genes involved in, i.e. photosynthesis, phosphate stress, antibiotic resistance, nitrogen fixation and vitamin biosynthesis. Geographic- BLAST can be used to investigate the presence of PhoH (accession YP 214558), a phosphate stress response gene, among the sequenced marine phages. The search results can then be interpreted in their environmental context, either as (i) average annual phosphate measurements, or (ii) stability of phosphate concentrations in terms of monthly SD (Figure 2c and d). A closer look at a single genome sample site reveals that in situ temperature was not originally reported (Figure 2e), whereas the interpolated data supplements this parameter, among others (Figure 5.2f). Web Services The newly extended version of megx.net offers programmatic access to MegDB content via Web Services, a powerful feature for experienced users and developers. All geographical maps can be retrieved via simple web requests, as specified by the Web Map Service (WMS) standard. The base URL for WMS requests is http://www.megx.net/ wms/gms, where more detailed information on how to use this service can be found. Megx.net also provides access to MIGS/MIMS reports in Genomic Contextual Data Markup Language (GCDML) XML files for all marine phage genomes through similar HTTP queries, e.g. http: //www.megx.net/gcdml/Prochlorococcus_phage_P-SSP7.xml [Field et al., 2008, Kottmann et al., 2008]. Other changes The massive influx of sequence data in the last years will out-compete the ability of scientists to analyze it [Anonymous, 2009]. This development already pushes megx.net’s capability to provide comprehensive pre-computed data to the limit. To better focus on integration of molecular sequence, contextual and environmental data, megx.net no longer offers pre-computed analyses, especially considering that other facilities, such as MG-RAST and CAMERA have emerged. Furthermore, the ‘EasyGenomes Browser’ has been replaced with links to the
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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
Page 31 and 32: 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
Page 45: 2.6. Conclusion 37 RK advised progr
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
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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
Page 77 and 78: 5.3. New database structure and con
Page 79 and 80: 5.3. New database structure and con
Page 81: 5.4. User Access 73 5.4 User Access
Page 85: 5.5. Summary 77 access charge: Max
Page 88 and 89: 80 6. Domains of unknown function 6
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Page 97 and 98: 7.2. GSC standards development 89 T
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Page 106 and 107: 98 8. Conclusion and outlook nities
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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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