MethTools 2.0

Please cite: Grunau et al. Nucleic Acids Res. 2000 Mar 1;28(5):1053-8.

Your bisulfite generated sequence data can be processed via this web page. | 2006 © Christoph Grunau | Server Statistics | Description: [PDF]

1. Generate the input file

  1. ALIGNMENT: you align your sequences i.e. the original unconverted sequence (mother sequence) and your bisulfite converted sequences either by hand or with your favorite alignment program. The Staden packadge or ClustalW can be used for this purpose. Click here to download a matrix that facilitates the alignment (please refer to the ClustalW manual for the use of external matrices).
  2. EDITING: manual editing of the alignment will be necessary in most cases. Make sure to bring all sequences to equal length - e.g. by adding "-" to the ends. The mother sequence is expected to have no internal gaps. Unknown bases can be represented by "n".
  3. SAVING: Save the sequences in FASTA format into one file "filename" as text file. The unconverted mother sequence has to be the first sequences. If you are uncertain about the required format, please have a look at our example or download the example file.

2. Enter your email address

email:

3. Choose your input file in concatenated FASTA/text-format.

If your browser does not display a button to choose a file it is probably not capable of understanding the HTML 4.0 protocol. Please replace it with the most recent version of Firefox.

(File names must not contain [spaces] or non-alphanumeric signs different from "." and "_".)

4. The methylation density distribution has to be calculated based on

.

5. Choose the file format for returned text files

6. Choose which files you wish to receive

5mC patterns as  images

5mCpG patterns as postscript and PDF images

sequence files

5mC desity plot as Gif image

5mCpN patterns as postscript and PDF images

error report

table with methylation profile

table with information content and LOGO

count C and 5mC

Note: If you select the SVG image format, you need a suitable vector graphics editor (e.g. Inkscape) to view the picture.

7. Click on the button

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