Supplementary Files

• This page includes the supplementary files for 'Germline Methylation Patterns Inferred from Local Nucleotides Frequency of Repetitive Sequences in Human Genome" (Kim et al. Mamm. Genome, in press).
  　
• Three kinds of information for the reproduction of the results, are available. The basic parameters such as (di)nucleotide frequencies, element size, RepeatMasker results (repeat sequence annotation, divergence, genomic coordinates) are provided in plain text format (tab separated).
  　
• Note that the genomic coordinates and related information (i.e. annotation of repeat sequences) are from the UCSC genome browser (2004, May freeze)

  - Here is the basic descriptions on the supplementary files (ReadMe.txt).
  - All files are plain tab-separated text files compressed with WinZip.

  1. (Di)nucleotide frequences related with germline methylation as well as other general information for total human transposable elements (~4,200,000)
  - The (sub)classification of transposable elements and divergence rates from consensus are according to UCSC genome browser (as the results of RepeatMasker program/database of RepBase)
  - Due to the large amount of data, the database is divided into four subsets according to their assigned chromosomes.

  - Repeat_TotalInfo_1.zip (Chromosome 1-4)

  - Repeat_TotalInfo_2.zip (Chromosome 5-9)

  - Repeat_TotalInfo_3.zip (Chromosome 10-16)

  - Repeat_TotalInfo_4.zip (Chromosome 17-22, X and Y)

  2. Three major classes of human repeats (Alu, L1 and LTR) located within 3000 bp from neighboring CpG islands.
  - Note that Alus and L1s are the dominant and recently amplified families of SINE and LINE (short and long interspersed nuclear element, respectively).
  - The distance from CpG islands was calculated with the closest CpG islands for individual elements, and those located within 3000 bp from nearby CpG islands were selected and provdied.

  - AluLess3000fromCpGisland.zip

  - L1Less3000fromCpGisland.zip

  - LTRLess3000fromCpGisland.zip

  3. The information of ~220,000 Alu pairs with basic information.
  - 220,000 Alu pairs (two Alu elements less separated by 650 bp) were classified into two pairs; inverted (two Alu elements have divergent convergent orientation, tail-to-tail or head-to-dead) and direct (two Alu elements have parallel orientation) pairs.
  - Using BLAST algorithm (bl2seq.exe), the 'homologous segment' within two Alu elements in determined (used Perl scripts are available on request). The separating distance (bp) and sequence homology (%) between homologous segments are then calculated and used to further classify the Alu pairs.

  - AluPair_Info.zip

  　

  Note: For any question or request for Perl scripts, please contact the developer.