Table 1

Comparison of different software functions for CpG island

Year of publication

2011

2006

2003

2002

2000


Software

CpGPAP

CpGcluster

CpGIS

CpGProD

CpGPlot


Reference

[22]

[8]

[7]

[6]

[5]


Availability

http://140.127.113. 93/CpGPAP/ webcite

http://bioinfo2.ugr. es/CpGcluster/ webcite

http://cpgislands.usc.edu/ webcite

http://pbil.univ-lyon1.fr/softwar e/cpgprod_quer webcite

http://www.ebi.ac.uk/Tools/emboss/cpgp webcite


F

u

n

c

t

i

o

n

Type

Web-based

Web-based

Web-based

Web-

based

Web-

based


Parameters

settings


CpG island result


CpG dinucleotides


TSS


O/E ratio bar


GC% bar


Upload sequence


Data integrator


Standalone


version


Method

CPSO and

CGA

cluster

Sliding

window

Sliding

window

Sliding

window


TSS: transcription start site. CPSO: complementary particle swarm optimization. CGA: complementary genetic algorithm

Chuang et al. BMC Genetics 2012 13:13   doi:10.1186/1471-2156-13-13

Open Data