daemon@ig.UUCP (11/10/87)
From: Terry Friedemann <FRIEDEMANN@BIONET-20.ARPA>
*********** Announcing New Experimental Distributed Software *************
We are pleased to announce a new experimental version of FASTP on the Dec2065
that allows a BIONET user to send mail to one of our SUN computers to do a
remote FASTP search. This version is still very experimental and while we
are fixing the last quirks we'd like your feedback on output and other cosmetic
things. For instance, would you like to see 10 or 50 of the top ranked scores
instead of 20?
Following is a sample interaction of FASTP Mail with a copy of the
sample file used at the end. You may use any sequence data you wish,
but please follow the simple file format shown. The alignment and
other output still needs a little fine tuning but will, along with
user input, be modified in the next few days hopefully.
FASTP Mail is one way that we hope to download some of the heavy load
on the DEC2065 to other computer resources. I'd like to thank Bill
Pearson, Warren Gish, David Roode, Jean-Pierre Dautricourt, and
especially Rob Liebschutz for all their help preparing FASTP Mail.
Terry Friedemann
Senior Applications Analyst
BIONET
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
To use FASTP Mail just enter the mm program:
@mm <cr>
MM>s <cr> ;and use the send command as for any other mail message
To:fastp@presto.ig.com ;this is the mail address to send your file to.
cc: ;presto is the name of the SUN computer.
Subject:test run
Message (End with ESCAPE or CTRL/Z.
Use CTRL/B to insert a file, CTRL/E to enter editor, CTRL/K to
redisplay message, CTRL/l to clear screen and redisplay, CTRL/N
to abort.):
^B ;hit control B to insert file
(Insert file: dl20.aa <cr> ;enter file name and hit carriage return
...EOF)
$ ;enter control Z or hit escape to get send
;prompt
SEND>s <cr> ;send data file to fastp program on the
;SUN (presto).
FRIEDEMANN@BIONET-20.ARPA.#Internet -- queued
fastp@PRESTO.IG.COM.#Internet -- queued
There is 1 additional message
N 11) 9-Nov To: fastp@PREST test run (512 chars)
You will then see:
N 12) 9-Nov daemon@presto.i Result of FASTP run (30273 chars)
MM> r 12
9-Nov-87 08:46:36-PST,34984; 000000000001
Return-Path: <daemon@presto.ig.com>
Recieved: from presto.ig.com by BIONET-20.ARPA with TCP; Mon 9 Nov 87
Received: by presto.ig.com (5.54/1.14)
id AA18933; Mon, 9 Nov 87 08:51:39 PST
Date: Mon, 9 Nov 87 08:51:39 PST
From: daemon@presto.ig.com
Message-Id: <8711091651.AA18933@presto.ig.com>
To: friedemann@BIONET-20.IG.COM
Subject: Result of FASTP run
Using protein library: protein.seq
/tmp/fastp.input.018929: 152 amino acids
/tmp/fastp.input.018929, 152 aa vs. protein.seq library
Score Count
< 2 0 :
4 0 :
6 0 :
8 11 :======
10 42 :=====================
12 127 :==================================================
14 391 :==================================================
16 477 :==================================================
18 641 :==================================================
20 716 :==================================================
22 676 :==================================================
24 521 :==================================================
26 294 :==================================================
28 223 :==================================================
30 151 :==================================================
32 102 :==================================================
34 59 :==============================
36 41 :=====================
38 20 :==========
40 2 :=
42 10 :=====
44 4 :==
46 4 :==
48 2 :=
50 1 :=
52 0 :
54 0 :
56 0 :
58 0 :
60 0 :
62 0 :
64 1 :=
66 0 :
68 0 :
70 0 :
72 0 :
74 0 :
76 0 :
78 0 :
80 1 :=
> 80 8 :====
/tmp/fastp.input.020804, 152 aa vs. protein.seq library
1274319 residues in 4525 sequences. Mean score (s.d.): 20.6 (5.52)
502 scores better than 27 saved. ktup: 2, fact: 8 scan time: 0:00:16.55
Filename in which to save results? [do not save] How many scores would you like to see? [20] The best scores are: init, opt
>P1:LCPG 96, 266
>P1:LCBO 96, 281
>P1:LCSH 96, 291
>P1:STPG 94, 103
>P1:STRT 93, 160
>P1:STHO 93, 160
>P1:STBO 92, 161
>P1:LCHU 85, 270
>P1:LCRT 80, 244
>P1:VCLJSA 63, 71
>P1:HAGC 49, 63
...... (rest of file)
Test run data file, dl20.aa:
>Linzer
WILLLLLVNSSLLWKNVASFPMCAMRNGRCFMSFEDTFELAGSLSHNISIEVSELFTEF
KHYSNVSGLRDKSPMRCNTSFLPTPENKEQARLTHYSALLKSGAMILDAWESPLDDLVS
LSTIKNVPDIIISKATDIKKKINAVRNGVNALMSTMLQNGDEEKKNPAWFLQSDNEDAR
HSLYGMISCLDNDFKKVDIYLNVLKCYMLKIDNC
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