iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data

BMC Genomics

Table 2 Evaluation of accuracy and CPU time of iSeeRNA, PhyloCSF, and CPC on comparison dataset

Dataset	Data size	Accuracy (%)			Running Time^c
		iSeeRNA		CPC^b	iSeeRNA	PhyloCSF^d	CPC
lincRNAs	2485	96.1	82.9	99.2	19.2s	3270m	278s
PCTs	2432	95.3	92.0	85.2	25.7s	13307m	309s

^a PhyloCSF failed to calculate the score for 34 lincRNAs; the accuracy and CPU time were thus calculated based on 2451 lincRNAs.
^b Uniref90 was used as the protein database.
^c m, minute; s, second.
^d To save the running time, we split the comparison dataset and ran PhyloCSF on 20 nodes in parallel. The reported CPU time was the sum of the execution time on all nodes.

ISSN: 1471-2164