Research article
CpGcluster: a distance-based algorithm for CpG-island detection
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* Corresponding author: José L Oliver oliver@ugr.es
1 Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Spain
2 Dpto. de Ingeniería Mecánica y Minera, Universidad de Jaén, Spain
3 Dpto de Física Aplicada II, Universidad de Málaga, Spain
4 Dpto. de Matemática Aplicada, Facultad de Ciencias, Universidad de Granada, Spain
5 Dept. of Molecular Biophysics, German Cancer Research Center, Heidelberg, Germany
BMC Bioinformatics 2006, 7:446 doi:10.1186/1471-2105-7-446
Published: 12 October 2006Additional files
Additional file 1:
Alignment with SERPINB5 promoter. Sequence alignment between the promoter of SERPINB5 (SPR, associated with a GC-rich region) and the CGI predicted by CpGcluster. None of the remaining CGI finders were able to detect any CGI in this region. The transcription start site (TSS), as given by the DBTSS data base [34], is shown in bold type.
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Additional file 2:
Distribution of distances between neighboring CpG dinucleotides in the human chromosomes 1 to 6
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Additional file 3:
Distribution of distances between neighboring CpG dinucleotides in the human chromosomes 7 to 12
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Additional file 4:
Distribution of distances between neighboring CpG dinucleotides in the human chromosomes 13 to 18
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Additional file 5:
Distribution of distances between neighboring CpG dinucleotides in the human chromosomes 19 to Y
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Additional file 6:
Comparison between analytical and experimental randomization. Length distribution of clusters with different numbers of CpGs. The analytical distribution (black line) is virtually identical to the experimental one obtained by a randomization that preserves the CpG frequency.
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