makeCGI 1.3.4 – Finding CpG Islands from DNA Sequences

makeCGI 1.3.4

:: DESCRIPTION

makeCGI is an R software package to obtain CGI from a genome. It fits two HMMs on GC content and observed to expected CpG ratio iteratively and obtain posterior probabilities for genomic regions being CpG islands. The CpG islands are then defined by thresholding the posterior probabilities.

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows /Linux/ MacOsX
R

:: DOWNLOAD

makeCGI

:: MORE INFORMATION

Citation

Wu H, Caffo B, Jaffe HA, Feinberg AP, Irizarry RA (2010)
Redefining CpG Islands Using a Hierarchical Hidden Markov Model.
Biostatistics 11(3): 499-514.

COHCAP 1.38.0 – City of Hope CpG Island Analysis Pipeline

COHCAP 1.38.0

:: DESCRIPTION

COHCAP is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

::DEVELOPER

Charles Warden <cwarden45 at gmail.com>

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux/MacOsX
JRE/ R

:: DOWNLOAD

COHCAP

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jun;41(11):e117. doi: 10.1093/nar/gkt242
COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis.
Warden CD1, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC.

CpGcluster 2.0 – CpG-island Detection

CpGcluster 2.0

:: DESCRIPTION

CpGcluster is a distance-based algorithm for CpG-island detection.CpGcluster uses only integer arithmetic, thus being a fast and computationally efficient algorithm able to predict statistically significant clusters of CpG dinucleotides. Another outstanding feature is that all predicted CGIs start and end with a CpG dinucleotide, which should be appropriate for a genomic feature whose functionality is based precisely on CpG dinucleotides.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX/Windows
Perl

:: DOWNLOAD

CpGcluster

:: MORE INFORMATION

Citation

Michael Hackenberg, Christopher Previti, Pedro L Luque-Escamilla, Pedro Carpena, José Martínez-Aroza and José L Oliver
CpGcluster: A distance-based algorithm for CpG-island detection
BMC Bioinformatics 7: 446, 2006

CpGProD – Predict Mammalian Promoters Associated with CpG Islands

CpGProD

:: DESCRIPTION

CpGProD (CpG Island Promoter Detection) is an application for identifying mammalian promoter regions associated with CpG islands in large genomic sequences. Although it is strictly dedicated to this particular promoter class corresponding to ≈50% of the genes, CpGProD exhibits a higher sensitivity and specificity than other tools used for promoter prediction. Notably, CpGProD uses different parameters according to species (human, mouse) studied. Moreover, CpGProD predicts the promoter orientation on the DNA strand.

CpGProD Online Version

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux

:: DOWNLOAD

CpGProD

:: MORE INFORMATION

Citation

Ponger, L. and Mouchiroud, D. (2001)
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences.
Bioinformatics, 18, 631-633

CgiHunter 1.0 – Exhaustive CpG Island Annotation

CgiHunter 1.0

:: DESCRIPTION

CgiHunter is a software for the annotation of CpG islands in genomic sequence. DNA sequence are accepted in FASTA format. The generated annotations are exhaustive i.e. all CpG island that matches the given parameters will be identified. CpG islands are genome regions with an elevated Guanine + Cytosine content (GC content) and a higher CpG dinucleotide frequency than observed in the bulk genome. More than half of the human gene promoters colocalize with CpG islands and their methylation status has been shown to correlate with the expression level of the associated genes. As a consequence, CpG islands are assumed to be hotspots of epigenetic regulation.

CgiHunter Online Version

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux / MacOsX
Python

:: DOWNLOAD

CgiHunter

:: MORE INFORMATION