Remote Analysis v1.2

While for routine analysis we strongly recommend to install the MethTools software package on your local computer, your bisulfite generated sequence data can also be processed via this web page. The resulting files will be send to you by email as attachment.

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. We use ClustalW for this purpose. At the Download page a matrix is provided whose use 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 Netscape. We do not recommend to use Internet Explorer since the file transfer from this browser is prone to errors. Please contact the authors if you encounter persistent error messages.

(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 png-images

(5m)CpG patterns as postscript graphs

sequence-files

5mC desity plot as png-image

5mCpN patterns as postscript graphs

error report

table with methylation profile

table with information content

7. Click on the button

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