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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.