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Table 5 Performance comparison: average time (in seconds) to insert all the Illumina HapMap data into the database and generate a PLINK “ped” file using dbVOR and SNPpy

From: dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets

Task

Cold Database

Hot Database

 

dbVOR

SNPpy

dbVOR

SNPpy

load all HapMap data

1311

1053

1302

1038

select all 620,932 marker

1333

586

1317

478

genotypes; write to ped file

    

select chromosome 1

117

188

98

111

genotypes; write to ped file

    

select chromosome 1 genotypes

28

235

8

112

between bp 500,000 to 1,000,000;

    

write to ped file

    
  1. The timings under Cold Database are for performing a task just after the database server is started. The Hot Database timing are for repeating the task a second (or third) time. The Cold numbers are averaged over three runs and the Hot numbers are averaged over six runs.
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BMC Bioinformatics

ISSN: 1471-2105

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