Data integration in microbial genomics ... - Jacobs University

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44 3. CDinFusion tiFASTA file with one CD set, and 3) Enriching subsets of sequences in a MultiFASTA file with several CD sets (Figure 3.1). The function- Figure 3.1: Overview of submission scenarios. Three primary scenarios of sequence data submission to INSDC can be distinguished and are all covered by the CDinFusion workflow: 1) The submission of a single FASTA sequence file along with one CD set, 2) The submission of a MultiFASTA file along with one CD set for all sequences in the file and 3) The submission of a MultiFASTA file annotated with several CD sets. ality of each of these different scenarios has been tested in dedicated use cases. The first use case was conducted with a single 16S rRNA sequence obtained from a bacterium isolated from a coastal water sample taken off the coast of the Wadden Sea island Sylt. After uploading the FASTA file the tool directly proceeded to the CD package selection for one CD set, as the file contained only a single sequence. The MIMARKS survey (mimarks s) package and the water package were selected to provide suitable CD fields for this environmental survey
3.3. Results 45 sequence obtained from seawater. Subsequently the web forms were Figure 3.2: CDinFusion web user interface. The CD are entered into the auto-generated web forms. Details about each parameter are accessible with the “more info” link. These details are retrieved using a web service accessing the GSC database and are therefore always up to date. filled with all the CD available for this particular sequence (example Figure 3.2). After generating and downloading the output file, the CD enriched FASTA was imported into Sequin version 11.00. CDinFusion inserted qualifiers specified by GenBank into the header line of the FASTA file. The tool placed the rest of the CD into a tab delimited structured comment file. This file was loaded into Sequin with the “Advanced Table Readers” option in the “Annotate” menu. The CD appeared in the metadata section between the header and the feature table section. By selecting “Done”, the Sequin file was saved and the complete submission was prepared. The INSDC database entry for this submission can be accessed at [Accession number: JF681370]. This use case exemplifies submission scenarios, where a single sequence and its CD are to be submitted to the INSDC databases. Single sequences can, for example, be marker genes or genomes that consist of a single sequence or contig. In the second use case, a permanent draft genome from a Rhodopirellula baltica strain along with its associated CD was prepared for submission. After the 6.9 Mb MultiFASTA file was uploaded, the user was
Page 1: Max Planck Institute for Marine Mic
Page 4 and 5: List of abbreviations BLAST Basic L
Page 6 and 7: Thesis abstract Deoxyribonucleic ac
Page 8 and 9: 4.2 Introduction . . . . . . . . .
Page 10 and 11: 2 1. Introduction syntax: data leve
Page 12 and 13: 4 1. Introduction used to derive ne
Page 14 and 15: 6 1. Introduction croorganisms thri
Page 16 and 17: 8 1. Introduction the middle at the
Page 18 and 19: 10 1. Introduction marker genes hel
Page 20 and 21: 12 1. Introduction what kind and wh
Page 22 and 23: 14 1. Introduction possibilities li
Page 24 and 25: 16 1. Introduction tual data acquis
Page 26 and 27: 18 1. Introduction Doug Wendel, Owe
Page 29 and 30: 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 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
Page 77 and 78: 5.3. New database structure and con
Page 79 and 80: 5.3. New database structure and con
Page 81 and 82: 5.4. User Access 73 5.4 User Access
Page 83 and 84: 5.4. User Access 75 tal context, co
Page 85: 5.5. Summary 77 access charge: Max
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
Page 101 and 102: 7.4. In silico Hypothesis Generatio
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7.5. Getting the most out of the da
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98 8. Conclusion and outlook nities
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100 8. Conclusion and outlook plina
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102 BIBLIOGRAPHY [Beynon-Davies, 20
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104 BIBLIOGRAPHY oceanic regions by
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106 BIBLIOGRAPHY [Giovannoni et al.
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108 BIBLIOGRAPHY [Kitano, 2002] Kit
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110 BIBLIOGRAPHY pathways in marine
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112 BIBLIOGRAPHY [Ramette, 2007] Ra
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114 BIBLIOGRAPHY (2006). Microbial
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116 BIBLIOGRAPHY [Williamson et al.
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CHAPTER 9 ACKNOWLEDGEMENTS First, I
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