Table 1 Peak detection algorithms investigated in the present study

PeakFinder 2.0.1

http://woldlab.caltech.edu/html/chipseq_peak_finder

[2]

S, C

none

GeneTrack 1.0.1

http://code.google.com/p/genetrack/

[9]

S

none

FindPeaks 3.1.9.2

http://www.bcgsc.ca/platform/bioinfo/software/findpeaks/

[6]

S

uniform

SISSRs

v1.4

http://sissrs.rajajothi.com/

[11]

S, C

Poisson/

control sample

QuEST

1.0

http://mendel.stanford.edu/sidowlab/downloads/quest/

[8]

C

control sample

MACS

1.3

http://liulab.dfci.harvard.edu/MACS/

[10]

S, C

local Poisson/

control sample

CisGenome

v1

http://www.biostat.jhsph.edu/~hji/cisgenome/

[5]

S, C

negative binomial/

control sample (binomial)

PeakSeq v1.01

http://www.gersteinlab.org/proj/PeakSeq/

[12]

C

local Poisson and

control sample (binomial)

Hpeak

1.1

http://www.sph.umich.edu/csg/qin/HPeak/

-

S, C

hidden Markov model