- for finding the region of interest:
island Searcher (D.Takai) screens DNA sequences for CpG islands
and generates a graphical output.
- for prediction of methylation probability:
- Methylator attempts to predict whether CpG in a DNA sequence are likely to be methylated or not.
- for primer design and verification:
(Long-Cheng Li) is a on-line tool for designing bisulfite-conversion-based
Methylation PCR Primers. It can design primers for Methylation-Specific
PCR (MSP) and Bisulfite-Sequencing PCR or Bisulfite-Restriction
PCR. The input sequence is DNA sequence in any format. The program
returns results in both text and graphic view.
provides access to a PCR primer-test and primer-design algorithm that can used for both bisulfite converted and not modified sequences. You can search various genomes with the designed primers by a fast ePCR method.
- Microsoft Word Macro for Analysis of Cytosine Methylation
made by Rakesh Singal, M.D.
This macro (i) converts genomic sequence to modified sequence that would
result after bisulfite treatment facilitating primer design for bisulfite
genomic sequencing and methylation-sensitive PCR assay and (ii) identifies
restriction sites that are preserved in bisulfite-converted and PCR-amplified
product only if cytosine residues at relevant CpG dinucleotides are methylated
(and thereby not converted to uracil) in the genomic DNA.
(Jo Vandesompele) allows you to check your primers for bisulfite
converted DNA by blasting them against the unmethylated and methylated
genomic sequences of man, mouse and rat. Work is in progress.
- for COmbined Bisulfite Restriction
- a tool for the selection of restriction enzymes for COBRA
- for analysis of bisulfite sequencing data:
- MethTools 1.x and MethTools 2.x
- collection of software tools for the analysis of bisulfite treated
DNA. The software does the comparison between unconverted mother sequences
and deaminated sequences, generates graphical outputs of methylation patterns
and methylation density, estimates the systematic error of the experiment
and searches for conserved methylated nucleotide-patterns. The software
can be used to generate files suitable for the submission to MethDB.
Analyzer (Christoph Bock) - this excellent java tool facilitates the
data analysis considerably. A must for each bisulfiter.
Generates archive files that can directly be uploaded to MethDB.
(Ian Carr) - a Windows program for the interactive editing of the bisulfite derived sequences that are aligned to a reference sequence.
- analysis of bisulfite sequencing. Results are send back by email.
- Bisulfite Sequencing DNA Methylation Analysis at the University of Bremen
- for integration of your data into the distributed
annotation system (DAS)
Other information sources
- Dirpedia.com - combining a dictionary, an encyclopedia and a web directory