MS DOS Molecular Biology Software on EMBL File Server
-----------------------------------------------------
Molecular biological software for IBM PC and clones is available from the
EMBL File Server. Though all programs are tested we can make no warranty on
the functionality of these programs nor shall be liable for any damage
resulting from their usage.
Most programs on the File Server are freeware, but that does not imply that
there are no rights reserved by the authors. Some programs are shareware. You
may freely copy and distribute these programs, but if you like to use them
after a trial period you are asked to send the author a small fee. Please see
the accompanying documentation files or manuals for details of copyright
status.
To get any file from the EMBL File Server use normal E-mail addressed to
NETSERV at EMBL-Heidelberg.DE. The body of the mail message should contain one
server command per line.
Getting started
---------------
MS DOS software on the EMBL File Server is distributed in a form that is
first compressed and then converted from binary to printable ASCII code
("uuencoded"). The standard extension for uuencoded files is ".uue". We
recommend the use of Dumas' UUD program for decoding ".uue" files.
How to get this program?
a) You have access to a C compiler:
Then download the source code for UUD by sending the command line:
GET DOS_SOFTWARE:UUD.C
Transfer it to your PC (e. g. using Kermit) and compile it.
b) You have access to a Pascal compiler or to GWBASIC:
Get the source code for a bootstrap uudecoder using
GET DOS_SOFTWARE:UUD19.BAS or
GET DOS_SOFTWARE:UUDECODE.PAS (resp.)
Transfer it to your PC and compile it.
These decoders can now in turn be used to get a copy of the recommended
decoder UUD.EXE from the EMBL File Server. First request the file
UUEMBL.UUE:
GET DOS_SOFTWARE:UUEMBL.UUE
Again, transfer this file to your PC and use either UUD19.COM or
UUDECODE.EXE to decode it:
> UUD19 UUEMBL.UUE or
> UUDECODE UUEMBL.UUE (resp.)
You will get a file called UUEMBL.EXE. Run it, and it will extract itself
to yield the UUD.EXE decoder and additionally the program UUE.EXE that is
used to create the .UUE files at the EMBL. Use UUD.EXE for all further
ASCII-binary conversions.
We tested UUD.C with Turbo C and UUDECODE.PAS with Turbo Pascal. If you have
problems compiling these sources with other compilers, please contact us.
Note for users in the UK:
While passing through the JANET/EARN gateway mail messages are often
corrupted by character conversions. The caret character is replaced by a
tilde. These conversions are not detected by UUD19. UUD19 will decode
UUEMBL.UUE without an error message, but the resulting UUEMBL.EXE program
will cause a system crash. Therefore check the UUEMBL.UUE file for
occurrences of the tilde character and replace them by caret characters
before decoding it.
How to access files
-------------------
All software for MS DOS on the EMBL File Server is in server directory called
DOS_SOFTWARE, and a directory listing can be acquired with the file server
command:
DIR DOS_SOFTWARE
To get any specific file use the command:
GET DOS_SOFTWARE:filename.ext
Transfer this file to your PC (e. g. using kermit). For decoding a uuencoded
file run UUD and specify the source file name:
> UUD filename.UUE
Files larger than 100K are split into parts. The first part is designated
"filename.UAA", the second part "filename.UAB" and so forth. If you send a
request for "filename.UAA", you will automatically receive all parts of a
package. The Subject line will tell you the part number of each part and how
many parts were sent in total. Only UUD will automatically join the related
files in correct order. The code generated from UUDECODE.PAS or UUD19.BAS
does *NOT* support file splitting. To decode split files follow this
procedure:
Extract all files from your mail reader to your disk. Call part 1 of a package
"filename.UAA", part 2 "filename.UAB", and so on. Transfer them to your PC.
Make sure that all belonging parts are in one directory and type:
> UUD filename.UAA
The name of the resulting file after UUDecoding is stored within the ".uaa" or
".uue" file; it will be placed in your current directory.
The outcome of this procedure is a so-called "self-extracting archive" with
a filename "filename.EXE". Just run it and it will create the final program
and documentation files:
> filename
Attention: the filename of the archive may in some cases be different from
the filename of the UUE or UAA files and may contain an additional "$" dollar
character. Check that by doing a DIR *.EXE after the uudecoding.
Record of requests
------------------
To facilitate communication between users of provided software and to give
software authors some information on who has obtained copies of their
programs, the File Server keeps a log of requests for each program by storing
the sender's E-mail address in a file named "filename.LOG". For example, to
get the log for the MSDOS program OLIGO use the command:
GET DOS_SOFTWARE:OLIGO.LOG
Problems
--------
If you have any problems or questions contact:
EMBL Data Library
Meyerhofstr. 1
D-6900 Heidelberg, FRG
tel.: +49-6221-387258
E-mail: SOFTWARE at EMBL-Heidelberg.DE
Directory of MS DOS Molecular Biology Software on EMBL File Server
------------------------------------------------------------------
To receive files from this directory use the command:
GET DOS_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename ALX3.UAA
update 17-Nov-1989
version 1.0
size 140 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Gotoh O.
description Alignment of three protein or DNA sequences
literature J. Theor. Biol. 121 (1986), 327-337
source code -
sw requirements -
hw requirements -
filename AUTHORIN.UAA
update 18-Jan-1992
version Release 1.2, v0.1
size 510 k
compressed LHARC (self-extracting)
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author IntelliGenetics
description Tool for preparing sequence data submissions
literature -
source code -
sw requirements -
hw requirements -
filename BIGMOUTH.UAA
update 13-Feb-1990
version -
size 235 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Jenson H. B.
description Digitized sounds and utilities for TypeSeq and DigiSeq
literature -
source code -
sw requirements DigiSeq or TypeSeq
hw requirements BigMouth sound digitizer
filename CIP.UUE
update 16-Jan-1990
version -
size 65 k
compressed PAK
ASCII conversion UUE
author Jenson H. B.
description Calculation of reaction conditions for dephosphorylation
literature -
source code -
sw requirements -
hw requirements -
filename CLONES.UAA
update 7-Mar-1990
version -
size 190 k
compressed PAK
ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC)
author Jenson H. B.
description Management of clones, strains, libraries etc. databases
literature BioTechniques 7 (1989), 590-592
source code -
sw requirements -
hw requirements -
filename CLUSTALV.UAA
update 6-Sep-1991
version 5
size 280 k
compressed ZOO
ASCII conversion UUE (split; will be sent in 4 parts: .UAA to .UAD)
author Higgins D., Fuchs R. and Bleasby A.J.
description Multiple sequence alignments
literature CABIOS 8 (1992), 189-191
source code C
sw requirements -
hw requirements -
filename CM.UAA
update 17-Dec-1991
version 1.0
size 800 k
compressed PAK
ASCII conversion UUE (split; will be sent in 8 parts: .UAA to .UAH)
author Hofmann K.
description Graphically oriented restriction map construction from
multiple digestion data
literature -
source code Pascal
sw requirements (Turbo Pascal for recompiling)
hw requirements Mouse
filename CMOLECUL.UUE
update 6-Oct-1989
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literature Nucleic Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements CGA card
filename CODONS.UUE
update 28-Jul-1992
version 1.4
size 95 k
compressed PAK
ASCII conversion UUE
author Lloyd A.T. and Sharp P.M.
description Codon usage analysis
literature J. Hered. 83 (1992), 239-240
source code -
sw requirements -
hw requirements -
filename COSY.UAA
update 6-Feb-1991
version 4.0
size 1100 k
compressed PAK
ASCII conversion UUE (split; will be sent in 25 parts: .UAA to .UAY)
author Eberhard M.
description Enzyme kinetics package
lite
