CpGcluster: a distance-based algorithm for CpG-island detection

doi:10.1186/1471-2105-7-446

BMC Bioinformatics

Volume 7

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Hackenberg M
Previti C
Luque-Escamilla PL
Carpena P
Martínez-Aroza J
Oliver JL

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Carpena P
Martínez-Aroza J
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Research article

CpGcluster: a distance-based algorithm for CpG-island detection

Michael Hackenberg¹ , Christopher Previti¹^,5 , Pedro Luis Luque-Escamilla² , Pedro Carpena³ , José Martínez-Aroza⁴ and José L Oliver¹

¹Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Spain

²Dpto. de Ingeniería Mecánica y Minera, Universidad de Jaén, Spain

³Dpto de Física Aplicada II, Universidad de Málaga, Spain

⁴Dpto. de Matemática Aplicada, Facultad de Ciencias, Universidad de Granada, Spain

⁵Dept. of Molecular Biophysics, German Cancer Research Center, Heidelberg, Germany

author email corresponding author email

BMC Bioinformatics 2006, 7:446doi:10.1186/1471-2105-7-446


Published:	12 October 2006

Additional 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.