PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

BMC Bioinformatics

Table 3 Comparison of computational performances of PLEK, CNCI, CPC and PhyloCSF

Performance	PLEK	CNCI	CPC	PhyloCSF
Run time^a (seconds)	128	1048	31247	181925^e
Multi-threading^b	Yes	Yes	No^d	No
Online running^c	No	No	Yes	No

Computational time was tested on 1,000 human mRNA transcripts and 1,000 human lncRNA transcripts.
^aComputation time consumed when run in a single-threading manner.
^bCan the software tool run in a multi-threading manner?
^cDoes the software tool provide a website for users to run online?
^dCPC improves its computational performance using a page-cache method on its website.
^eBed files were load onto the Galaxy webserver (http://galaxy.nbic.nl/) and the tool ‘Stitch Gene Blocks’ was used to retrieve multiple alignment files with sequence entries for the following genome builds based on the 10-way Multiz alignment to hg19: hg19, panTro2, tarSyr1, micMur1, otoGar1 and rheMac2. PhyloCSF was run using the options: --removeRefGaps.

ISSN: 1471-2105