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Instructions



In order to use the NetPlantGene server for splice site prediction in Plant DNA:
  1. Select a local Fasta file by pressing the 'Browse...' bottom. Remember to make the correct file selection mask (like *.fasta). A fasta file is an ASCII file with the sequence, as shown below, and should contain only one sequence.
  2. The fasta file must be submitted using the one letter abbreviations for the nucleotides: `acgtuACGTU' or 'X' for unknown.
  3. The sequence must be more than 200 (preferably more than 250) and less than 80.000 nucleotides long. Shorter sequences are accepted, but the prediction will be suboptimal. Long sequences may provoke a time out. In such cases use the mail server (NetPlantGene@cbs.dtu.dk). Send a mail with the word "help" to the mail server to get help.
  4. Press the "Send file" button.
  5. A WWW page will return the results as the prediction finishes. Response time depends on system load.

EXAMPLE FASTA FILE

The first line must start with the symbol '>', the next word on that line is used as the sequence identifier. The following lines should contain the actual sequence, consisting of the symbols A, T, U, G, C and X. U is converted to T, letters not mentioned are converted to X. All letters are converted to upper case. Numbers, blanks and other nonletter symbols are skipped. The lines should not be longer than 80 characters.

>sequenceident
ACGACCGTGACGTGCAGTAGTGGACGATTAGCTGATGCTAGCGGCGATCGATCGTCAGT
GCAGCTGATTAGCGGCTAGCTGACTTACGCGCGGATCATTTCTAGCGTAGCTAGCTGAC
ACGTACGGCTATTATGCTACTTAGCTGACTTATTAGGCCTATATGCGATGCTATGCTAG
CGAGCAATCGCCTACAGTATGATTAGACTTTCGAGTCGATACTCGATGCTAGCTAGTGC
CGATCGATTCGATTCGATTCG



GETTING HELP

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