MethTools 2.0

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 package or ClustalW can be used for this purpose. 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:

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

*NOTE: File names must not contain [spaces] or non-alphanumeric signs different from "." and "_".

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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  gif svg png no  images**
• 5mCpG patterns as postscript and PDF images
• sequence files
• 5mC density 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

7. Click on the button