D A P M A I L
=============
DAPMAIL is a program that gives remote access to the Edinburgh University
Biocomputing Research Unit (BRU) fast sequence database searching programs that
runs on an Active Memory Technology Distributed Array Processor AMT DAP.
To use DAPMAIL, send electronic mail to one of the following
addresses :-
dapmail@uk.ac.ed
dapmail@uk.ac.ed.biocomp
dapmail@uk.ac.edinburgh
dapmail@uk.ac.edinburgh.biocomputing
Your computer system should be set up so that you can contact at least
one of these addresses. If this does not appear to be the case please consult
your local system support staff or else contact the BRU.
It is also important for your system to be able to receive return mail from
the Edinburgh system; please check initially by requesting 'help' and
verifying you can receive the message from Edinburgh. The output file
may be quite big; check regularly that you have enough space in yuor system
to receive a big (up to 100Kbyte) file.
In order for your message to be understood correctly by the Edinburgh
program it must be in a special format which I will now describe.
1) Subject field : (Optional). You may like to use it to contain
something like a title for your job.
It will be retained in the output.
2) Choice of Command: (Compulsory) This is the command you wish executed.
Currently the following are available.
prosrch - runs the protein database search program
using a query sequence.
ptnsrch - runs the protein database search program.
using a query pattern.
diasrch - runs the NA database search program
using a query sequence.
help - gets you this file
news - gets you a file of current news re dap searches
& available resources.
3) For search commands like prosrch & ptnsrch, there are optional
lines, each with two parts: the first is the name of a
relevent parameter and the second its value.
Currently the following are available for prosrch:
pams
indel
noise
database
PAMS has range 1 - 500. Strongly recommended not to exceed 250.
has default of 100.
INDEL has default value depending on PAM value chosen.
Only respecify it once you know what this default is.
NOISE has default of 0.0; it has range 0 - 2.0, and non-zero
values help discriminate between likely alignments of
interest, and alignments representing probably only noise.
DATABASE will default to the latest swiss-prot database. Others
may be available. Check for news item.
The following are available for ptnsrch:
pams
indel
database
PAMS has range 1 - 500. Strongly recommended not to exceed 100.
has default of 100.
INDEL has default value depending on PAM value chosen.
Only respecify it once you know what this default is.
DATABASE will default to the latest swiss-prot database. Others
may be available. Check for news item.
4) For search commands like prosrch & ptnsrch, there is one
Compulsory word, on a line by itself:
sequence.
5) Your sequence data now follows in one of the following formats
for prosrch:
plain - just the sequence on any number of line
nbrf - a single line identifier(starting with >)
a single line description
the sequence on any number of lines
wisc - a UGWGCG format sequence file.
For ptnsrch:
plain - just the sequence on any number of line
pattern - the pattern of amino-acids specifiying one or
more residue at each position in the peptide chain.
Where several residues are acceptable at a location,
they are shown in the line of text within round
brackets.
Example Message
=======
prosrch
indel -10
sequence
ADHGTYERTWIDISDGHHGFD
<...>
ptnsrch
pams 50
indel -20
sequence
A(DE)HG(ST)YERT(FYW)IDISDGHHGFD
<...>
John Collins
Edinburgh University Biocomputing Research Unit
April 1993
End of message
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