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Table 2 Data integration time of different methods

From: VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants

Method Integrating variant Integrating variant flanking
  locations (second) windows (second)
BigBed 277.90 275.63
Interval tree 0.41 0.60
Relational database 8.05 736.23
Tabix 8.87 8.88
Our algorithms 0.21 0.52
  1. For BigBed reader and interval tree, we used the implementation of bxpython. For relational database, we tried several indexing methods including standard B-tree index and spatial index, and report here the shortest time among these approaches. Tabix was called using the pytabix library in Python.