🚀 go-pugleaf

 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@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 second.
                     structure properties are plotted.
literatur            CABIOS, in prep.
source code          -
sw requirements      MATLAB-PC
hw requirements      Math. co-processor, >2M RAM

filename             LIGATE.UUE
version              -
size                 75 k
compressed           PAK
ASCII conversion     UUE
author               Jenson, H. B.
description          Calculation of reaction conditions for ligation
literatur            BioTechniques 5 (1987), 729-730
source code          -
sw requirements      -
hw requirements      -

filename             MOLECSRC.UUE
version              May 87
size                 70 k
compressed           PAK
ASCII conversion     UUE
author               Thompson J. R. (Cedergren R.)
description          Source code for *MOLECUL.UUE
literatur            Nucl. Acids Res. 10 (1982), 8351-8356
source code          Pascal
sw requirements      Turbo Pascal
hw requirements      -

filename             MOTIF.UUE
version              - (bug fix with plain ASCII sequences)
size                 45 k
compressed           PAK
ASCII conversion     UUE
author               Giles I.
description          Motif searching program
literatur            CABIOS 5 (1989), 227-232
source code          C
sw requirements      (Turbo C for recompiling)
hw requirements      -

filename             OLIGO.UUE
version              1.0
size                 105 k
compressed           PAK
ASCII conversion     UUE
author               Beadles K.
description          Oligo-directed single amino acid substitution
literatur            -
source code          -
sw requirements      -
hw requirements      -

filename             PATTERN.UUE
version              -
size                 55 k
compressed           PAK
ASCII conversion     UUE
author               Giles I.
description          Pattern searching program
literatur            CABIOS 5 (1989), 227-232
source code          C
sw requirements      (Turbo C for recompiling)
hw requirements      -

filename             PCFOLD.UUE
version              4.0
size                 160 k
compressed           PAK
ASCII conversion     UUE
author               Zuker M.
description          RNA folding
literatur            Meth. Enzymology 180 (1989), 262-288
source code          Fortran, Asm
sw requirements      (Compiler for recompiling)
hw requirements      -

filename             PLASMID.UUE
version              1.1
size                 75 k
compressed           PAK
ASCII conversion     UUE
author               Lipsick J.
description          Plasmid drawing program (CGA card req.)
literatur            -
source code          Basic
sw requirements      (Quickbasic for recompiling)
hw requirements      CGA card

filename             PREDICT.UUE
version              1.2
size                 120 k
compressed           PAK
ASCII conversion     UUE
author               Carmenes R. S.
description          Protein secondary structure predictions
literatur            Biochem. Biophy. Res. Commun. 15 (1989), 687-698
source code          -
sw requirements      -
hw requirements      -

filename             PRONET.UUE
version              1.0
size                 110 k
compressed           PAK
ASCII conversion     UUE
author               Pascarella S.
description          protein structure prediction with a neural network
literatur            CABIOS 5 (1989), 319-320
source code          Pascal
sw requirements      (Turbo Pascal for recompiling)
hw requirements      -

filename             SDSE.UAA
version              2.0
size                 185 k
compressed           PAK
ASCII conversion     UUE (split)
author               Oliver J. L.
description          Simulation of DNA sequence evolution (Part 1 of 2)
literatur            CABIOS 5 (1989), 47-50
source code          -
sw requirements      -
hw requirements      -

filename             SDSE.UAB
version              2.0
size                 50 k
compressed           PAK
ASCII conversion     UUE (split)
author               Oliver J. L.
description          Simulation of DNA sequence evolution (Part 2 of 2)
literatur            CABIOS 5 (1989), 47-50
source code          -
sw requirements      -
hw requirements      -

filename             SEQAID.UUE
version              3.6
size                 360 k
compressed           PAK
ASCII conversion     UUE
author               Roufa D.
description          DNA and protein sequence analysis package
literatur            -
source code          -
sw requirements      -
hw requirements      -

filename             SIGSEQ.UUE
version              1.0
size                 60 k
compressed           PAK
ASCII conversion     UUE
author               Popowicz A.M.
description          Prediction of signal sequence cleavage site
literatur            CABIOS 4 (1988), 405-406
source code          C
sw requirements      (Compiler for recompiling)
hw requirements      -

filename             TDALIGN.UUE
version              1.61
size                 120 k
compressed           PAK
ASCII conversion     UUE
author               Davison D. (Thompson K.)
description          Sequence alignment
literatur            -
source code          -
sw requirements      -
hw requirements      -

filename             TYPESEQ.UUE
version              -
size                 55 k
compressed           PAK
ASCII conversion     UUE
author               Jenson, H. B.
description          Sequence input using keyboard
literatur            CABIOS 4 (1988), 218
source code          -
sw requirements      -
hw requirements      -

(b) Archiving/Decoding Software

filename             UUEMBL.UUE
version              -
size                 35 k
compressed           PAK
ASCII conversion     UUE
author               Fuchs R. (Dumas M.)
description          UUEncoded form of UUD uudecoder and UUE uuencoder
literatur            -
source code          C
sw requirements      -
hw requirements      -

filename             UUD.C
version              -
size                 20 k
compressed           no
ASCII conversion     no
author               Dumas M.
description          Source code for recommended uudecoder
literatur            -
source code          C
sw requirements      Turbo C
hw requirements      -

filename             UUDECODE.PAS
version              modified 4-Dec-1989
size                 6 k
compressed           no
ASCII conversion     no
author               -
description          Source code for bootstrap uudecoder
literatur            -
source code          Pascal
sw requirements      Turbo Pascal
hw requirements      -

filename             UUD19.BAS
version              -
size                 5 k
compressed           no
ASCII conversion     no
author               -
description          Source code for bootstrap uudecoder
literatur            -
source code          Basic
sw requirements      GWBasic
hw requirements      -

filename             DETAR.UUE
version              -
size                 45 k
compressed           PAK
ASCII conversion     UUE
author               VALVERDE J. R.
description          Utility to extract .TAR files
literatur            -
source code          C
sw requirements      Turbo C (for recompiling)
hw requirements      -

Files with the extension ".uue", ".uaa" etc. must be decoded with UUD.
See HELP DOS_SOFTWARE for details.

To get a listing of *all* software files available from the EMBL File Server
send the command GET ALL_SOFTWARE to NETSERV@EMBL.