From: SJJ@ICBR.IFAS.UFL.EDU ("JONG, SONG-MUH J")
Newsgroups: bionet.software
Subject: Re. Mol. Biol. Software Request
Date: 22 Dec 92 20:35:00 GMT
Distribution: bionet


 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@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@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
literature           CABIOS 6 (1990), 213-221
source code          Pascal
sw requirements      -
hw requirements      -

filename             CREGEX.C
update               7-Oct-1992
version              1.2
size                 10 k
compressed           -
ASCII conversion     -
author               Leunissen J.
description          Reformating of Prosite for use with Kolakowski's PROSEARCH
literature           -
source code          C
sw requirements      (used by PROSEARCH [PROSEA12.UAA])
hw requirements      -

filename             CUTCOST.UAA
update               5-Jun-1991
version              2.31
size                 105 k
compressed           PAK
ASCII conversion     UUE
author               Meinhof C. G.
description          Identification of cheapest source for restriction enzymes
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             DIGISEQ.UUE
update               13-Feb-1990
version              -
size                 80 k
compressed           PAK
ASCII conversion     UUE
author               Jenson H. B.
description          Sequence input using digitizer
literature           CABIOS 4 (1988), 218
source code          -
sw requirements      -
hw requirements      Graf/Bar 7 digitizing device

filename             DNACLONE.UAA
update               16-Mar-1990
version              1.1
size                 190 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 3 parts: .UAA to .UAC)
author               Roy T. K.
description          Management of clones, strains, libraries etc. databases
literature           CABIOS 5 (1989), 321-322
source code          -
sw requirements      -
hw requirements      -

filename             DNAFRAG.UUE
update               31-Jan-1992
version              3.03
size                 30 k
compressed           PAK
ASCII conversion     UUE
author               Nash J.
description          Measures molecule size of gel bands from standards
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             DOTPLOT.UUE
update               17-Sep-1992
version              2.0
size                 85 k
compressed           PAK
ASCII conversion     UUE
author               Nakisa R.
description          Dot plot analysis
literature           -
source code          -
sw requirements      -
hw requirements      EGA or VGA card

filename             EASYCLON.UAA
update               11-Jul-1991
version              1.0
size                 145 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Shillitoe E. J.
description          Simulation of DNA cloning incl. plasmid map drawing
literature           Biotechniques 10 (1991), 768-770
source code          -
sw requirements      -
hw requirements      -

filename             EASISTAT.UAA
update               15-Feb-1991
version              1.2
size                 350 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 5 parts: .UAA to .UAE)
author               Curtis D.
description          Package for statistical analyses
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             ELBAMAP.UUE
update               5-Jan-1990
version              2.2
size                 55 k
compressed           PAK
ASCII conversion     UUE
author               King G. J.
description          Management of electrophoresis banding patterns
literature           CABIOS 5 (1989), 313-317
source code          -
sw requirements      -
hw requirements      EGA card

filename             EMOLECUL.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      EGA card

filename             ENZKIN.UAA
update               16-Aug-1990
version              1.0
size                 120 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Maloy S. R.
description          Enzyme kinetics calculation
literature           CABIOS 6 (1990), 63-65
source code          Fortran
sw requirements      -
hw requirements      Math co-processor

filename             EPIPLOT.UAA
update               12-Jul-1990
version              1.0
size                 128 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Menendez-Arias L.
description          Prediction of B and T cell epitopes from protein sequences
literature           CABIOS 6 (1990), 101-105
source code          -
sw requirements      -
hw requirements      -

filename             ESEE.UAA
update               1-Jul-1992
version              1.09e
size                 210 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 3 parts: .UAA to .UAC)
author               Cabot E.L.
description          Multiple sequence editor
literature           CABIOS 5 (1989), 233-234
source code          -
sw requirements      -
hw requirements      -

filename             EZ-FIT.UAA
update               18-Oct-1989
version              1.1
size                 170 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Perella F. W.
description          Calculation of enzyme and receptor kinetics
literature           Anal. Biochem. 174 (1989), 437-447
source code          -
sw requirements      -
hw requirements      CGA card

filename             FAST.UAA
update               26-Jan-1990
version              -
size                 195 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 3 parts: .UAA to .UAC)
author               Facchiano A.
description          Protein structure analysis
literature           CABIOS 5 (1989), 299-303
source code          -
sw requirements      -
hw requirements      CGA or EGA/VGA card

filename             FASTMAP.UAA
update               28-Jul-1992
version              1
size                 190 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 3 parts: .UAA to .UAC)
author               Curtis D.
description          Approx. multipoint lod score calculation
literature           Human Heredity (submitted)
source code          -
sw requirements      -
hw requirements      -

filename             GEL.UUE
update               18-Oct-1989
version              17-Feb-1989
size                 50 k
compressed           PAK
ASCII conversion     UUE
author               Thompson J. R.
description          Calculation of DNA restriction fragment sizes
literature           Anal. Biochem. 115 (81), 113-122
source code          Pascal
sw requirements      (Turbo Pascal for recompiling)
hw requirements      -

filename             GEL-JML.UAA
update               15-Apr-1992
version              1.1
size                 160 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Lacroix J. M.
description          Calculation of DNA restriction fragment sizes
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             GMD.TXT
update               22-Jan-1992
version              -
size                 25 k
compressed           -
ASCII conversion     -
author               Fu Y. and Arnold J.
description          Programs to assist in the design of genome mapping
                     experiments (contig mapping)
literature           Biometrics, in press
source code          Fortran
sw requirements      Fortran compiler for recompilation
hw requirements      -

filename             HMOLECUL.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      Hercules card

filename             HYDRASC.UUE
update               8-Oct-1989
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.
literature           CABIOS, in prep.
source code          -
sw requirements      MATLAB-PC
hw requirements      Math. co-processor, >2M RAM

filename             LIGATE.UUE
update               16-Jan-1990
version              -
size                 75 k
compressed           PAK
ASCII conversion     UUE
author               Jenson H. B.
description          Calculation of reaction conditions for ligation
literature           BioTechniques 5 (1987), 729-730
source code          -
sw requirements      -
hw requirements      -

filename             LSTSQ.UAA
update               25-Sep-1991
version              1.10
size                 500 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 6 parts: .UAA to .UAF)
author               Carmenes R. S.
description          Toolkit for nonlinear regression in enzymology
literature           CABIOS 7 (1991), 373-378
source code          C, Pascal and Modula-2
sw requirements      -
hw requirements      -

filename             MACAW103.UAA
update               15-Apr-1992
version              1.03
size                 190 k
compressed           PAK
ASCII conversion     UUE
author               Schuler G.
description          Multiple sequence editor
literature           Proteins 9 (1991), 180-191
source code          -
sw requirements      MS Windows
hw requirements      -

filename             MAPSRT.UUE
update               2-Jul-1991
version              1.0
size                 40 k
compressed           PAK
ASCII conversion     UUE
author               Easton T. G.
description          Reformats GCG MapSort output file to new style,
                     sorted by number-of-cuts and enzyme name.
literature           -
source code          Pascal
sw requirements      -
hw requirements      -

filename             MARKER.UUE
update               31-Jan-1992
version              1.1
size                 90 k
compressed           PAK
ASCII conversion     UUE
author               Rensing S.
description          Creation of restriction fragments banding pattern and
                     DNA length standards
literature           -
source code          Pascal
sw requirements      -
hw requirements      -

filename             MARS.UAA
update               18-Jul-1990
version              -
size                 120 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               De Boer J. G.
description          Finds sites in DNA which can easily be changed into
                     a restriction site by one or two changes
literature           CABIOS 7 (1991), 267
source code          -
sw requirements      -
hw requirements      -

filename             MELPROT.UUE
update               27-Mar-1990
version              -
size                 80 k
compressed           PAK
ASCII conversion     UUE
author               Sikaris K.
description          Secondary structure prediction and plotting
literature           CABIOS 5 (1989), 323
source code          Basic
sw requirements      Any Basic interpreter
hw requirements      -

filename             MELT.UUE
update               25-May-1990
version              2.0
size                 30 k
compressed           PAK
ASCII conversion     UUE
author               Nash J.H.E.
description          Melting point calculation of oligonucleotides
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             MISMATCH.TXT
update               15-Apr-1992
version              ?
size                 12 k
compressed           -
ASCII conversion     -
author               Davidow L. S.
description          Selection of PCR designed mismatch primers
literature           CABIOS 8 (1992), 193
source code          Basic
sw requirements      Basic interpreter/compiler
hw requirements      -

filename             MOLECSRC.UUE
update               6-Oct-1990
version              May 87
size                 70 k
compressed           PAK
ASCII conversion     UUE
author               Thompson J. R. (Cedergren R.)
description          Source code for *MOLECUL.UUE
literature           Nucleic Acids Res. 10 (1982), 8351-8356
source code          Pascal
sw requirements      Turbo Pascal
hw requirements      -

filename             MOTIF.UUE
update               8-Nov-1989
version              - (bug fix with plain ASCII sequences)
size                 45 k
compressed           PAK
ASCII conversion     UUE
author               Giles I.
description          Motif searching program
literature           CABIOS 5 (1989), 227-232
source code          C
sw requirements      (Turbo C for recompiling)
hw requirements      -

filename             MULTALIN.UAA
update               2-Apr-1990
version              3.0
size                 130 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Corpet F.
description          Multiple sequence alignment
literature           Nucleic Acids Res. 16 (1988), 10881-10890
source code          -
sw requirements      -
hw requirements      -

filename             NUMCLONE.UUE
update               26-Feb-1992
version              1.0
size                 30 k
compressed           LHArc
ASCII conversion     UUE
author               Nash J.H.E.
description          Estimates the number of clones one has to screen from a
                     genomic library in order to find a desired clone
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             OLIGO.UAA
update               6-Oct-1989
version              1.0
size                 105 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Beadles K.
description          Oligo-directed single amino acid substitution
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             PATTERN.UUE
update               9-Nov-1989
version              -
size                 55 k
compressed           PAK
ASCII conversion     UUE
author               Giles I.
description          Pattern searching program
literature           CABIOS 5 (1989), 227-232
source code          C
sw requirements      (Turbo C for recompiling)
hw requirements      -

filename             PCFOLD.UAA
update               23-Oct-1989
version              4.0
size                 160 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Zuker M.
description          RNA folding
literature           Meth. Enzymology 180 (1989), 262-288
source code          -
sw requirements      -
hw requirements      -

filename             PEDRAW14.UAA
update               28-Jul-1992
version              1.4
size                 410 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 5 parts: .UAA to .UAE)
author               Curtis D.
description          Pedigree drawing program
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             PLASMID.UUE
update               6-Oct-1989
version              1.1
size                 75 k
compressed           PAK
ASCII conversion     UUE
author               Lipsick J.
description          Plasmid drawing program
literature           -
source code          Basic
sw requirements      (Quickbasic for recompiling)
hw requirements      CGA card

filename             PLASMIDG.UAA
update               11-Jul-1991
version              1.0
size                 140 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Kleman G.
description          Plasmid drawing program
literature           -
source code          Pascal
sw requirements      -
hw requirements      Microsoft-compatible mouse

filename             PREDICT.UAA
update               20-Feb-1990
version              1.2
size                 120 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Carmenes R. S.
description          Protein secondary structure predictions
literature           Biochem. Biophy. Res. Commun. 15 (1989), 687-698 
source code          -
sw requirements      -
hw requirements      -

filename             PRIMGEN.UUE
update               14-Apr-1992
version              1.1
size                 60 k
compressed           PAK
ASCII conversion     UUE
author               Nash J. H. E.
description          Oligonucleotide primer design by reverse-translation of
                     amino acid sequences
literature           CABIOS, submitted
source code          -
sw requirements      -
hw requirements      VGA or EGA graphics card required

filename             PROGRAPH.UAA
update               27-Nov-1991
version              1.3
size                 810 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 8 parts: .UAA to .UAH)
author               Hofmann K.
description          Graphically oriented protein sequence analysis package
literature           CABIOS 8 (1992), 331-338
source code          Pascal
sw requirements      (Turbo Pascal for recompiling)
hw requirements      Mouse

filename             PRONET.UAA
update               23-Jan-1990
version              1.0
size                 110 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Pascarella S.
description          Protein structure prediction with a neural network
literature           CABIOS 5 (1989), 319-320
source code          Pascal
sw requirements      (Turbo Pascal for recompiling)
hw requirements      -

filename             PROSEA12.UAA
update               24-Jan-1991
version              1.2
size                 100 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Kolakowski L. F.
description          Pattern searching in proteins using Prosite
literature           -
source code          C
sw requirements      Awk
hw requirements      -

filename             RAMHA.UAA
update               28-Jul-1992
version              1.0
size                 120 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Siderovski, D.P.
description          Monte Carlo simulation of the random mutagenesis of
                     synthetic cDNA
literature           CABIOS, submitted
source code          -
sw requirements      -
hw requirements      -

filename             SAR2PCIT.UUE
update               31-Aug-1992
version              1.0
size                 20 k
compressed           PAK
ASCII conversion     UUE
author               Sonnhammer, E.L.
description          Converts SeqAnalRef to ProCite format
literature           -
source code          Pascal
sw requirements      -
hw requirements      -

filename             SDSE.UAA
update               24-Nov-1989
version              2.0
size                 185 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 3 parts: .UAA to .UAC)
author               Oliver J. L.
description          Simulation of DNA sequence evolution
literature           CABIOS 5 (1989), 47-50
source code          -
sw requirements      -
hw requirements      -

filename             SIGSEQ.UUE
update               11-Dec-1989
version              1.0
size                 60 k
compressed           PAK
ASCII conversion     UUE
author               Popowicz A.M.
description          Prediction of signal sequence cleavage site
literature           CABIOS 4 (1988), 405-406
source code          C
sw requirements      (Compiler for recompiling)
hw requirements      -

filename             SIM.UUE
update               12-Feb-1991
version              -
size                 30 k
compressed           PAK
ASCII conversion     UUE
author               Huang G. and Miller W.
description          Local similarity searching
literature           CABIOS 6 (1990), 373 - 381.
source code          C
sw requirements      -
hw requirements      -

filename             SORFIND.UAA
update               31-Aug-1992
version              1.6
size                 105 k
compressed           PKZIP
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Hutchinson G.B.
description          Prediction of exons in vertebrate genomic DNA
literature           Nucleic Acids Res. 20 (1992), 3453-3462
source code          -
sw requirements      -
hw requirements      -

filename             SQAID381.UAA
update               1-Aug-1991
version              3.81
size                 300 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 4 parts: .UAA to .UAD)
author               Roufa D.
description          DNA and protein sequence analysis package
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             SSCAN.UAA
update               3-Apr-1992
version              3.0
size                 340 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 4 parts: .UAA to .UAD)
author               Prestridge D.
description          Signal Scan: a program to identify known eukaryotic
                     signals in DNA sequences
literature           CABIOS 7 (1991), 203-206
source code          C
sw requirements      -
hw requirements      -

filename             SUBSIS.UUE
update               18-May-1990
version              1.2
size                 15 k
compressed           PAK
ASCII conversion     UUE
author               Mandler J.
description          Subdirectory handling with DNASIS(tm) or PROSIS(tm)
literature           CABIOS 6 (1990), 291-292
source code          GWBASIC
sw requirements      GWBASIC, DNASIS or PROSIS, MS-DOS DEBUG
hw requirements      -

filename             TDALIGN.UAA
update               18-Nov-1989
version              1.61
size                 120 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Davison D. (Thompson K.)
description          Sequence alignment
literature           -
source code          -
sw requirements      -
hw requirements      -

filename             TFD2PROSITE.C
update               13-Dec-1991
version              1.3
size                 10 k
compressed           -
ASCII conversion     -
author               Fuchs R.
description          Program to convert SITES and DOMAINS tables of TFD
                     database to Prosite format.
literature           -
source code          C
sw requirements      -
hw requirements      -

filename             TRBBS.UAA
update               21-Sep-1992
version              1.0
size                 120 k
compressed           PAK
ASCII conversion     UUE (split; will be sent in 2 parts: .UAA and .UAB)
author               Consani I.R.
description          File exchange program for automated fluorescent DNA
                     sequencer data
literature           CABIOS 8 (1992), 195.
source code          -
sw requirements      -
hw requirements      VGA video card

filename             TYPESEQ.UUE
update               13-Feb-1990
version              -
size                 55 k
compressed           PAK
ASCII conversion     UUE
author               Jenson H. B.
description          Sequence input using keyboard
literature           CABIOS 4 (1988), 218
source code          -
sw requirements      -
hw requirements      -

(b) Archiving/Decoding Software

filename             UUEMBL.UUE
update               6-Feb-1991
version              -
size                 60 k
compressed           PAK
ASCII conversion     UUE
author               Fuchs R. (Dumas M.)
description          UUEncoded form of UUD uudecoder and UUE uuencoder 
literature           -
source code          C
sw requirements      -
hw requirements      -

filename             UUD.C
update               6-Feb-1991
version              -
size                 20 k
compressed           no
ASCII conversion     no
author               Dumas M.
description          Source code for recommended uudecoder
literature           -
source code          C
sw requirements      Turbo C
hw requirements      -

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

filename             UUD19.BAS
update               6-Oct-1989
version              -
size                 5 k
compressed           no
ASCII conversion     no
author               -
description          Source code for bootstrap uudecoder
literature           -
source code          Basic
sw requirements      GWBasic
hw requirements      -

filename             DETAR.UUE
update               2-Mar-1990
version              -
size                 45 k
compressed           PAK
ASCII conversion     UUE
author               VALVERDE J. R.
description          Utility to extract .TAR files
literature           -
source code          C
sw requirements      Turbo C (for recompiling)
hw requirements      -

filename             PRNTGL.UAA
update               23-Feb-1992
version              1.18
size                 150 k
compressed           PAK
ASCII conversion     UUE
author               Ravitz, C.
description          Prints HGPL files (like produced by GCG) on matrix or
                     laser printer
literature           -
source code          -
sw requirements      -
hw requirements      -

7-Oct-1992