Data integration in microbial genomics ... - Jacobs University

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42 3. CDinFusion sortium (GSC), an international consortium, which promotes mechanisms to standardize the description of genomes and the exchange of genomic data, to create a series of checklists defining the minimal set of CD that should accompany a sequence submission. The Minimum Information About a (Meta)Genome Sequence (MIGS/MIMS) checklist [Field et al., 2008] outlines a conceptual structure for extending the core information that has been traditionally captured by the INSDC (DDBJ/EMBL/GenBank) to describe genomic and metagenomic sequences. The Minimum Information about a MARKer gene Sequence (MIMARKS) standard complements the MIGS/MIMS specification by adding two new “report types”, a ”MIMARKS-survey” and a ”MIMARKS-specimen”, the former being the checklist for uncultured diversity marker gene surveys, the latter is designed for marker gene sequences obtained from any material identifiable via specimens. The standards also cover sets of measurements and observations describing particular habitats, termed ”environmental packages”. Collectively the MIGS/MIMS/MIMARKS standards are now called MIxS (Minimum Information about any (x) Sequence) (Yilmaz et al., The Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications, accepted). Through collaboration with the GSC, the INSDC now offers the structures to store the data items specified in the GSC checklists. This facilitates an early integration of sequence data and CD. However, specialized tools to allow this integration for different user scenarios are needed. The European Nucleotide Archive (ENA) provides an on-line submission system called Webin which contains prepared web forms for the submission of GSC compliant data. It shows all fields with descriptions, explanations and examples and does data validation in the forms (https://www.ebi.ac.uk/embl/genomes/submission/login.jsf, accessed: 16.03.2011). The Investigation Study Assay (ISA) Infrastructure offers a software suite that produces documents that can be submitted to the Sequence Read Archive (SRA) repository [Rocca-Serra et al., 2010]. With the Quantitative Insights Into Microbial Ecology (QIIME) web application [Caporaso et al., 2010] users can generate and validate MIMARKS-compliant templates. Finally, MetaBar is a
3.3. Results 43 spreadsheet and web-based software tool which assists users in the consistent acquisition, electronic storage and submission of CD associated to their samples [Hankeln et al., 2010]. However, a tool that integrates CD and sequence data by directly enriching FASTA files for submission does not exist yet. Here we present CDinFusion (Contextual Data and FASTA in fusion). CDinFusion has been designed to submit sequence data together with CD to INSDC. CDinFusion intends to facilitate the integration of CD and sequence data prior to submission by directly enriching sequence data using the FASTA format. It generates submission-ready outputs for INSDC by implementing the MIxS standard defined by the GSC. CDinFusion processes single as well as MultiFASTA files, containing up to millions of sequences. It was successfully applied to several use cases. Example submissions to the INSDC can be accessed with the following accession numbers: JF681370, JF268327-JF268425 and Genome Project ID 63253. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology, Bremen, Germany: http://www.megx.net/cdinfusion. The tool is easy to install and released under the LGPL 3 open source license to promote distribution in aid of increasing the quantity and quality of CD in the public repositories. 3.3 Results CDinFusion has been designed as a web-based tool, which enables users to upload single or MultiFASTA files from single sequence to highthroughput analysis and enrich them with CD. After uploading the sequences, the user is requested to select the appropriate GSC checklist and environmental package. CD can be entered in the web forms or CSV templates can be downloaded, filled with CD off-line and uploaded. The CSV files help to store and share the data. The merged sequence and CD can be downloaded for subsequent submission to INSDC. The implemented workflow covers the three typical scenarios of sequence submission to an INSDC database namely: 1) Enriching a single sequence with one CD set, 2) Enriching many sequences in a Mul-
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 . . . . . . . . .
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Page 39 and 40: 2.5. Discussion 31 taking samples i
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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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Data integration in microbial genomics ... - Jacobs University

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