SS BBB A SS EEEE H H EEEE L PPP
S S B B A A S S E H H E L P P
S B B A A S E H H E L P P
S BB AAAAA S EEE HHHHH EEE L PPP
S B B A A S E H H E L P
S B B A A S E H H E L P
S S B B A A S S E H H E L P
SSS BBB A A SSS EEEE H H EEEE LLLL P
----------------------------------
This is the help file of the SBASE Email Server at the
International Centre for Genetic Engineering and Biotechnology
AREA Science Park, Padriciano 99, 34012 Trieste, Italy.
----------------------------------
The SBASE Email Server is at present experimental. Please send comments
to sbase-comment@icgeb.trieste.it. Thanks.
The SBASE e-mail server accepts a specially formatted mail message
containing a protein query sequence, and, as a response, it sends the list
of the most probable domain homologies. A database search is performed
against the SBASE library of protein domains using the BLAST algorithm,
and the search results, provided with annotations, are returned in a mail
message.
How to use:
Getting HELP:
============
This help file can be gotten by sending an email to
sbase@icgeb.trieste.it
containing the word HELP alone in the first line of the message body.
Making a QUERY:
===============
Send e-mail to sbase@icgeb.trieste.it using the example below
Note: the parameters before the token BEGIN are optional, (here the
defaults are listed), the lines after BEGIN are required.
Please note, that the server reads the sequence up to the first empty
line only and no further. (After all, the frequently appended signatures
do not make nice matchings.)
Example:
MATRIX PAM120
SCORE PARAMETER 35
ANNOTATIONS YES
BEGIN
> mysequence
LRNGVDINTCNQNGLNGLHLASKEGHVKMVVELLHKEIILETTTKKGNTALHIAALAGQDEVVRELVNYG
GLNGLHLASKEGHVKMVVELLHKEIILETTTKKGNTALHIAALAGQDEVVRELVNYG
One can easily produce this input by converting the sequence to FASTA
format then adding the parameters as shown above using any editor.
Other formats (for example GCG) are not supported yet.
Response time
=============
Requests are handled immediately, in serial order. At present, response
time is quite short and is restricted by the network load rather than CPU
availability.
Evaluation of the output:
=========================
The output of the server are BLAST search results against the SBASE
protein domain library.
Since this file can easily be bigger 50K to make the mail transfer safer
and faster we chop it up into smaller pieces. This puts the burden of
stripping the mail headers and concatenating the files together
onto the recipient.
The output file contains the BLAST search results, organized as follows:
1) List of the best scoring domain entries. As SBASE entries are named
by domain names (function, structure, etc.), this list already may give
some information on the expected domain composition.
2) List of alignments. For each SBASE entry you will find the complete
annotation of the domain, followed by one (or several) alignments with
(different parts of) the query. If one domain is found several times in
your query, you may find several alignments with the same or related
entries at different parts of the query. Please note that it depends on the
score parameter whether or not you see all the alignments. Do not use very
low cutoff values because that results in prohibitively long output
files. (For the time being, we have set the default cutoff to 35 and
the minimum cutoff to 30).
3) Run statistics. This is usually not essential for the evaluation of
the results; you can get a complete description of these and other blast
parameters by sending a HELP message to blast.ncbi.nlm.nih.gov
Important: Failure to see a homology with a known domain may be due to
several reasons: i) The domain type is not (yet) included in the SBASE
domain library; ii) The threshold score parameter was set too high for the
domain to be detected; iii) A different scoring matrix may be necessary in
order to detect the alignment with the domain type in question. In the present
experimental version of the SBASE server we support only the matrices used
by BLAST; "customized matrices" will be added later to the final version.
Papers to reference in reporting results:
=========================================
Pongor, S., Skerl, V., Cserzo, M. and Hatsagi, Z., Simon, G. and
Bevilacqua, V. (1992): The SBASE domain library release 2.0& A
collection of annotated protein sequence segments, Nucleic Acids. Res ,
21, 311-315
Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers,
and David J. Lipman (1990) Basic local alignment search tool J. Mol.
Biol. 215:403-410.
Software availability
=====================
The Sbase database is available by anonymous ftp at
ftp.icgeb.trieste.it:/pub/sbase2
The blast software is available by anonymous ftp at
ncbi.nlm.nih.gov:/pub/
Protection of your sequence data
================================
The query sequences are not stored in any form.
Further info:
=============
Server functions: Zsolt Hatsagi
Tel: +39-40-3757342
General info: Sandor Pongor
Tel: +39-40-3757300
FAX: +39-40-226-555
Mail: International Centre for Genetic Engineering
and Biotechnology
AREA Science Park, Padriciano 99
34012 Trieste, Italy
________________________________________