GOParGenPy: a high throughput method to generate Gene Ontology data matrices

BMC Bioinformatics

Table 2 Execution time of various available packages

Number of Genes	AnnotationDbi/GO.db Package in	GeneOntology package in	GOParGenPy
Number of Genes	R/Bioconductor	BIOPERL	GOParGenPy
80975	>592* sec	>300* sec	40 sec
21318390	d.n.f^#	d.n.f^#	3300 sec

Tests were performed on a 2.93GHz Intel Xeon X7350 with 64 GB RAM. Note that only GOParGenPy created also the output files in these tests, whereas the other packages only linked the annotations to the parent classes.
^* indicates the time taken by these packages only to generate the parent GO classes for given GO classes associated with these genes. ^# execution time was too long. d.n.f: did not finish.

ISSN: 1471-2105