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Usage instructions



1. Specify the input sequences

All the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:

A C D E F G H I K L M N P Q R S T V W Y and X (unknown)

All the alphabetic symbols not in the allowed alphabet will be converted to X before processing. All the non-alphabetic symbols, including white space and digits, will be ignored.

The sequences can be input in the following two ways:

  • Paste a single sequence (just the amino acids) or a number of sequences in FASTA format into the upper window of the main server page.

  • Select a FASTA file on your local disk, either by typing the file name into the lower window or by browsing the disk.

Both ways can be employed at the same time: all the specified sequences will be processed. However, there may be not more than 4,000 sequences and 2,000,000 amino acids in toto in one submission. The sequences may not be longer than 5,000 amino acids.


2. Customize your run

  • Regular expressions:
    In this field you can enter your own regular expression for filtering. A default expession is presented in the field.
    The default regular expression 'RR.[FGAVML][LITMVF]' means arginines in the two first positions, any amino acid in the third position, (F or G or A or V or M or L) in the forth position and finally any of the following amino acids in the fifth position (L or I or T or M or V or F).
    Character Name Meaning
    . dot Any amino acid is allowed
    [...] character class Amino acids listed between the brackets are allowed
    [^...] negated character class Amino acids listed between the brackets and the ^ are not allowed

  • Graphics output:
    No graphics, in line GIF or in line GIF and EPS as links. Click here for examples.

  • Text output:
    Standard, full od short output format. Click here for examples.

  • Sequence truncation:
    Signal peptides occurr at the N-terminal end of protein sequences; they are seldom longer than 45 amino acids. It is normally not meaningful to submit more than 60-70 amino acids per sequence. Therefore, the default truncation has been set to 70.

3. Submit the job

Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.

At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.




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