{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T01:48:48Z","timestamp":1760233728623,"version":"build-2065373602"},"reference-count":26,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2021,2,11]],"date-time":"2021-02-11T00:00:00Z","timestamp":1613001600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100018929","name":"German Network for Bioinformatics Infrastructure","doi-asserted-by":"publisher","award":["031L0103"],"award-info":[{"award-number":["031L0103"]}],"id":[{"id":"10.13039\/501100018929","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["11.000sz00.00.0 17 114347 0"],"award-info":[{"award-number":["11.000sz00.00.0 17 114347 0"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005908","name":"Bundesministerium f\u00fcr Ern\u00e4hrung und Landwirtschaft","doi-asserted-by":"publisher","award":["22404015"],"award-info":[{"award-number":["22404015"]}],"id":[{"id":"10.13039\/501100005908","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Algorithms"],"abstract":"<jats:p>Mass spectrometers enable identifying proteins in biological samples leading to biomarkers for biological process parameters and diseases. However, bioinformatic evaluation of the mass spectrometer data needs a standardized workflow and system that stores the protein sequences. Due to its standardization and maturity, relational systems are a great fit for storing protein sequences. Hence, in this work, we present a schema for distributed column-based database management systems using a column-oriented index to store sequence data. In order to achieve a high storage performance, it was necessary to choose a well-performing strategy for transforming the protein sequence data from the FASTA format to the new schema. Therefore, we applied an in-memory map, HDDmap, database engine, and extended radix tree and evaluated their performance. The results show that our proposed extended radix tree performs best regarding memory consumption and runtime. Hence, the radix tree is a suitable data structure for transforming protein sequences into the indexed schema.<\/jats:p>","DOI":"10.3390\/a14020059","type":"journal-article","created":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T16:12:10Z","timestamp":1613146330000},"page":"59","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An Investigation of Alternatives to Transform Protein Sequence Databases to a Columnar Index Schema"],"prefix":"10.3390","volume":"14","author":[{"given":"Roman","family":"Zoun","sequence":"first","affiliation":[{"name":"Line of Business Life Science, Adesso Schweiz AG, 8048 Z\u00fcrich, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1683-7222","authenticated-orcid":false,"given":"Kay","family":"Schallert","sequence":"additional","affiliation":[{"name":"Bioprocess Engineering, University of Magdeburg, 39106 Magdeburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9580-740X","authenticated-orcid":false,"given":"David","family":"Broneske","sequence":"additional","affiliation":[{"name":"Databases and Software Engineering, University of Magdeburg, 39106 Magdeburg, Germany"}]},{"given":"Ivayla","family":"Trifonova","sequence":"additional","affiliation":[{"name":"Line of Business Life Science, Adesso Schweiz AG, 8048 Z\u00fcrich, Switzerland"}]},{"given":"Xiao","family":"Chen","sequence":"additional","affiliation":[{"name":"Databases and Software Engineering, University of Magdeburg, 39106 Magdeburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7840-8899","authenticated-orcid":false,"given":"Robert","family":"Heyer","sequence":"additional","affiliation":[{"name":"Bioprocess Engineering, University of Magdeburg, 39106 Magdeburg, Germany"},{"name":"Databases and Software Engineering, University of Magdeburg, 39106 Magdeburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4021-8525","authenticated-orcid":false,"given":"Dirk","family":"Benndorf","sequence":"additional","affiliation":[{"name":"Bioprocess Engineering, University of Magdeburg, 39106 Magdeburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9576-8474","authenticated-orcid":false,"given":"Gunter","family":"Saake","sequence":"additional","affiliation":[{"name":"Databases and Software Engineering, University of Magdeburg, 39106 Magdeburg, Germany"}]}],"member":"1968","published-online":{"date-parts":[[2021,2,11]]},"reference":[{"key":"ref_1","unstructured":"(2021, February 10). 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[Ph.D. Thesis, Freie Universit\u00e4t Berlin]."}],"container-title":["Algorithms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4893\/14\/2\/59\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:22:45Z","timestamp":1760160165000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4893\/14\/2\/59"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,11]]},"references-count":26,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2]]}},"alternative-id":["a14020059"],"URL":"https:\/\/doi.org\/10.3390\/a14020059","relation":{},"ISSN":["1999-4893"],"issn-type":[{"type":"electronic","value":"1999-4893"}],"subject":[],"published":{"date-parts":[[2021,2,11]]}}}