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J Cell Biochem. 2015 Jun;116(6):877-83. doi: 10.1002/jcb.25049.

Benchmarking database performance for genomic data.

Author information

1
Bioinformatics Unit, Children's Medical Research Institute, Westmead, NSW, Australia; Centre for Cancer Research, Westmead Millennium Institute; Sydney Medical School, Westmead, University of Sydney, Sydney, Australia.

Abstract

Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene annotations are common research needs. The data can be saved in a database system for easy management, however, there is no comprehensive database built-in algorithm at present to identify overlapping regions. Therefore I have developed a novel region-mapping (RegMap) SQL-based algorithm to perform genomic operations and have benchmarked the performance of different databases. Benchmarking identified that PostgreSQL extracts overlapping regions much faster than MySQL. Insertion and data uploads in PostgreSQL were also better, although general searching capability of both databases was almost equivalent. In addition, using the algorithm pair-wise, overlaps of >1000 datasets of transcription factor binding sites and histone marks, collected from previous publications, were reported and it was found that HNF4G significantly co-locates with cohesin subunit STAG1 (SA1).Inc.

KEYWORDS:

DATABASE BENCHMARKING; EPIGENETIC MODIFICATIONS; MANAGING GENOMIC LOCATIONS DATA; REGMAP; TRANSCRIPTION FACTOR BINDING SITES

PMID:
25560631
DOI:
10.1002/jcb.25049
[Indexed for MEDLINE]

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