CpG_MI provides a useful information-theoretic tool to identify functional CpG islands from the CpG clusterings in the bulk genomes. The CpG islands of six mammals and four fishes are identified by CpG_MI for download. Due to CpG dinucleotide densities differ from organism to organism, the corresponding organism should be selected firstly for CpG_MI. CpG dinucleotides densities of different genomes are implicated in the dialog box of organism. Then you can identify CpG islands by three approaches: (I) inputing the start and end coordinate positions of a chromosome, or (II) pasting one sequence in FASTA format, or (III) uploading a fasta sequence file. The output of CpG_MI includes the CpG islands identified together with corresponding genome coordinates, length, number of CpGs, G+C content and CpG O/E of the CpG islands. You can also download the standalone version for long sequences.
Fetch sequences based on genomic coordinates (1-based) in specific version of genome assembly is welcome. Uploading a FASTA sequence via file or copying and pasting is also allowed, while the largest file size is set to be 1Mb and only the files with the extension name of .fasta, .fa, .txt are allowed.Please select the proper genome assembly, for the cutoffs are refined for different genomes. The executable PERL file is available for large sequences. Large sequence may take a title long time, please be patient (a 200kb sequence may take up to 4 minutes!). Enjoy yourself!
We have predicted CpG islands from ten organisms. The CpG islands can
be visualized in UCSC Genomic Browser.
Jianzhong Su, Project leader, algorithm development, Email:firstname.lastname@example.org
Jie Lv, middleware programming and frontend development, Email:email@example.com
Yan Zhang, deployment, web server administration, Email:firstname.lastname@example.org
Please cite:"Jianzhong Su, Yan Zhang, Jie Lv, Hongbo Liu, Xiaoyan Tang, Fang Wang, Yunfeng Qi, Yujia Feng and Xia Li, CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes (Nucleic Acids Research, 2010, 38(1):e6)".
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