In reply to one of Dan Davison's previous postings:
Indeed, some filenames on the EMBL File Server in the directory DOS_SOFTWARE
contained a dollar character ($). The reason is the following: All files in
that directory are delivered in a form compressed and converted to ASCII.
After the uudecoding you will get a so-called self-extracting archive which
is a standard executable MSDOS program that will create the actual files of
a software package during execution. Example: a hypothetic package consists
of files README.DOC and DOIT.COM. We will compress them using PAK to create
an archive called DOIT.EXE that will, when executed, produce the files
README.DOC and DOIT.COM again. And here is the problem. Suppose that the
name of DOIT.COM is in fact DOIT.EXE. Then PAK will try to create an archive
having the same file name! That is the simple reason why some archive names
have an additional $ character. It was only added to have a unique archive
name.
In the second step, when the archive files are converted to ASCII using UUE,
the resulting UUE files will have the same filename as the archive but the
extension .UUE instead of .EXE. Ie, they will also contain the dollar sign.
But in contrast to the first step here it is not really necessary to have
the dollar; it is just "inherited" during the conversion process.
It now turned out that there may be a problem with Kermit, translating the
dollar to some other character, especially when dealing with split uuencoded
files (in fact, this could only happen with CLONES). Therefore I have
removed all $ characters from the UUE file names (where they are not
required). But they will stay in the names of the archive files created
after decoding. Since we recommend that decoding should be done after
transferring the files to the PC, this should cause no problems.
The HELP DOS_SOFTWARE file has been updated accordingly. I include the
directory listing of DOS_SOFTWARE, now containing the new file names.
Finally, I'd like to point out that Jotun Hein's TREEALIGN multiple sequence
alignment and phylogeny program for VAX and UNIX is now available from the
server. It is split in two parts:
VAX_SOFTWARE:TREEALIG.UAA and VAX_SOFTWARE:TREEALIG.UAB
Rainer Fuchs, Ph.D.
EMBL Data Library
fuchs at embl.bitnet
DIR DOS_SOFTWARE
Attention: some filenames have been changed (removal of the dollar sign)
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.UUE
version 1.0
size 140 k
compressed PAK
ASCII conversion UUE
author Gotoh O.
description Alignment of three protein or DNA sequences
literatur J. Theor. Biol. 121 (1986), 327-337
source code -
sw requirements -
hw requirements -
filename BIGMOUTH.UUE
version -
size 235 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Digitized sounds and utilities for TypeSeq and DigiSeq
literatur -
source code -
sw requirements DigiSeq or TypeSeq
hw requirements BigMouth sound digitizer
filename CIP.UUE
version -
size 65 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Calculation of reaction conditions for dephosphorylation
literatur -
source code -
sw requirements -
hw requirements -
filename CLONES.UAA
version -
size 190 k
compressed PAK
ASCII conversion UUE (split)
author Jenson, H. B.
description Management of clones, strains, libraries etc. databases
(Part 1 of 2)
literatur BioTechniques 7 (1989), 590-592
source code -
sw requirements -
hw requirements -
filename CLONES.UAB
version -
size 45 k
compressed PAK
ASCII conversion UUE (split)
author Jenson, H. B.
description Management of clones, strains, libraries etc. databases
(Part 2 of 2)
literatur BioTechniques 7 (1989), 590-592
source code -
sw requirements -
hw requirements -
filename CMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements CGA card
filename DIGISEQ.UUE
version -
size 80 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Sequence input using digitizer
literatur CABIOS 4 (1988), 218
source code -
sw requirements -
hw requirements Graf/Bar 7 digitizing device
filename ELBAMAP.UUE
version 2.2
size 55 k
compressed PAK
ASCII conversion UUE
author King G. J.
description Management of electrophoresis banding patterns
literatur CABIOS 5 (1989), 313-317
source code -
sw requirements -
hw requirements EGA card
filename EMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements EGA card
filename EZ-FIT.UUE
version 1.1
size 170 k
compressed PAK
ASCII conversion UUE
author Perella F. W.
description Calculation of enzyme and receptor kinetics
literatur Anal. Biochem. 174 (1989), 437-447
source code -
sw requirements -
hw requirements CGA card
filename FAST.UUE
version -
size 195 k
compressed PAK
ASCII conversion UUE
author Facchiano, A.
description Protein structure analysis
literatur CABIOS 5 (1989), 299-303
source code -
sw requirements -
hw requirements CGA or EGA/VGA card
filename GEL.UUE
version 17.2.89
size 50 k
compressed PAK
ASCII conversion UUE
author Thompson J. R.
description Calculation of DNA restriction fragment sizes
literatur Anal. Biochem. 115 (81), 113-122
source code Pascal
sw requirements (Turbo Pascal for recompiling)
hw requirements -
filename HMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements Hercules card
filename HYDRASC.UUE
version 1
size 30 k
compressed PAK
ASCII conversion UUE
author Penttila T. J.
description Contour map for two polypeptide sequences.
Regions with similar hydropathic properties and sec
