Submitting Sequences Using E-mail

To submit a request via e-mail, put your protein sequence in a message formatted to look like the one in the "Example of an E-Mail Request" section below, and send to psa-request@darwin.bu.edu. As far as the PSA server is concerned, this is entirely equivalent to using the Web interface at "http://bmerc-www.bu.edu/psa/".

You may choose the modeling assumptions by including the line

    Analysis-assumptions: type

monomeric-soluble

selects Type-1 models;

minimal

selects Type-2 models; or

wd-repeat

selects WD-repeat models.

Similarly, the optional "PSA-Plot-Format:" field may specify PostScript (the default), PDF-2.1, or PDF-3.0. As for the "Analysis-Assumptions:" field, alphabetic case does not matter, for either the field name or the value. See the "psa-request Server Results" section for more information about these plot formats.

At present, there is no way to specify Web delivery of analysis results from an e-mail message.

Example of an E-Mail Request

	To: psa-request@darwin.bu.edu
  [1]	Subject: Seq 23
  [2]	Analysis-assumptions: monomeric-soluble

  [3]	; psa-plot-format: postscript
  [4]	; Wilson Brandlesnarf
	; BMERC
	; Boston MA
	; 617-353-7123
  [5]	Sequence 23
  [6]	GWEIPEPYVWDESFRVFYEQLDEEHKKIFKGIFDCIRDNSAPNLATLVKV
	TTNHFTHEEAMMDAAKYSEVVPHKKMHKDFLEKIGGLSAPVDAKNVDYCK
	EWLVNHIKGTDFKYKGKL

  [7]	Regards, Wilson

1. If you put the word "help" in the e-mail "Subject:" field (or in the body of your request), the server will interpret the message as a request for help instructions (and will ignore any sequence it might find in the body). In that case, you will receive a general information message, which includes the instructions you are now reading. Other than that, the "Subject:" field text is arbitrary; it will only be used to construct the subject fields of our replies to your request.

2. The optional "Analysis-Assumptions:" field (shown here in the e-mail header) may specify monomeric-soluble, minimal, or wd-repeat; see above for details.

3. The optional "PSA-Plot-Format:" field (shown here in the comments section) may specify PostScript, PDF-2.1, or PDF-3.0. Alphabetic case does not matter, for either the field name or the value. PostScript will be used by default. The psa-request server will return all plots in the requested format; see the "Results from the psa-request server" page for further details.

   Although the "Analysis-Assumptions:" field is shown in the e-mail header and the "PSA-Plot-Format:" is in in the comment section, either or both could be put in either place. This is handy, since some mail programs do not give the user any way to specify extra header fields.

   Note that if "Analysis-Assumptions:" and/or "PSA-Plot-Format:" appear in the comments section, they must appear before any other comment lines, or they will be recognized as comments rather than options.

4. Comment section. There must be at least one line that starts with a semicolon (';') character; without it, the server will not recognize the message body as containing an IG format sequence. All such semicolon lines are comments, which we suggest you use to list your name, affiliation, city, possibly a voice-mail number, etc. Empty comment lines (i.e. nothing after the semicolon) are OK.

   NB: Any blank lines after the start of the comment section will terminate the sequence.

5. Sequence label. There must be a label immediately following the last comment line. This is the name or label you choose for the sequence. In this example it is "Sequence 23". Because this label will used in the titles of graphs, we suggest that you use no more than about 15 characters. NB: There must be no semicolon in front of the label.

6. Protein sequence. The sequence itself must immediately follow the label. Each amino acid in the sequence is represented by its usual one-letter code (e.g., A = alanine), from the set {a, c, d, e, f, g, h, i, k, l, m, n, p, q, r, s, t, v, w, y}; upper and lower case letters are equivalent. The sequence may contain up to 1000 amino acids. A blank line terminates the sequence. You may include white space around and within the sequence (but watch out for blank lines!).

7. Anything else in the body of the message is ignored. This includes any other sequence information. Each sequence must be sent in a separate mail message.

If the submitted sequence contains illegal characters, or there is some other problem with the request, the server will generate a reply explaining the difficulty.

If the request is accepted by the server (i.e. is not a help request and has no syntax errors), you will receive a confirmation of your request via e-mail shortly after the server receives it, and the analysis results shortly thereafter.

In any case, you should expect a reply from the server within ten minutes or so, plus rountrip mail delivery time. If not, please doublecheck your e-mail address, and the "Lost psa-request results" page at http://bmerc-www.bu.edu/psa/lost.htm.

Go to:

• Submit a sequence analysis request.
• List of topics about the PSA server.
• The BMERC Home Page.

Please direct your questions and comments about these Web pages and the PSA e-mail server to: