Re. Mol. Biol. Software Request

JONG, SONG-MUH J SJJ at ICBR.IFAS.UFL.EDU
Tue Dec 22 15:35:00 EST 1992


 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



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