An Investigation of Alternatives to Transform Protein Sequence Databases to a Columnar Index Schema

Abstract

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.