An Investigation of Alternatives to Transform Protein Sequence Databases to a Columnar Index Schema
| Autor: | Gunter Saake, Roman Zoun, Xiao Chen, Dirk Benndorf, David Broneske, Robert Heyer, Ivayla Trifonova, Kay Schallert |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
radix tree
lcsh:T55.4-60.8 Computer science Radix tree sequence data computer.software_genre 01 natural sciences Column (database) lcsh:QA75.5-76.95 Theoretical Computer Science 03 medical and health sciences proteomics Trie lcsh:Industrial engineering. Management engineering mass spectrometry 030304 developmental biology Database engine 0303 health sciences Numerical Analysis Database 010401 analytical chemistry FASTA format trie Data structure 0104 chemical sciences Schema (genetic algorithms) Computational Mathematics Workflow Computational Theory and Mathematics storage system lcsh:Electronic computers. Computer science computer |
| Zdroj: | Algorithms, Vol 14, Iss 59, p 59 (2021) Algorithms Volume 14 Issue 2 |
| ISSN: | 1999-4893 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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