New software on the UH Gene-Server

Dan Davison Davison at UH.EDU
Wed Jun 26 23:21:13 EST 1991


A lot of software has been added to the UH Gene-Server in the past few
days. This note details the additions. There's something for everyone
here!

Note especially the multiple sequence alignment editors for VMS
(MALIGNED by Steve Clark), Unix (GDE, Genetic Data Environment by
Steve Smith) and PIMA,(Pattern Induced Multiple Alignment by Randy
Smith), and the Mac (MSE, by Ralph Gonzalez).  You now have no excuse
not to have one...


All files are now avaiable via anonymous FTP from menudo.uh.edu,
129.7.1.6, in ~ftp/pub/genbank-server/vms, unix, dos, or mac.

N.B. All GenBank files have been updated also.

VMS:

 204800 Jun 26 22:19 maligned.uue  Steve Clark's MALIGNED multiple
                                   sequence alignment editor (great name!)
                                   Note the size...
  91921 Jun 26 22:12 scrutine.uaa  Newest SCRUTINEER, analysis for VMS
  91922 Jun 26 22:12 scrutine.uab
  91922 Jun 26 22:12 scrutine.uac
  91922 Jun 26 22:12 scrutine.uad
  91922 Jun 26 22:12 scrutine.uae
  91922 Jun 26 22:12 scrutine.uaf
  91922 Jun 26 22:12 scrutine.uag
  91922 Jun 26 22:12 scrutine.uah
  91922 Jun 26 22:12 scrutine.uai
  91923 Jun 26 22:12 scrutine.uaj
  91923 Jun 26 22:12 scrutine.uak
  22754 Jun 26 22:12 scrutine.ual
  84071 Jun 26 22:26 boxshade.uue K. Hoffman's shading sequence pgm



MAC

     97986 Jun 26 22:01 dbconv1.hqx  Convert flat file to tab-delimited
     46765 Jun 26 22:01 dbconv2.hqx  by J. Valverde
     97990 Jun 26 22:01 embl-search1.hqx R. Fuchs db retrieval for EMBL
     48613 Jun 26 22:01 embl-search2.hqx   CD-ROM only
     97988 Jun 26 22:00 seqspeak1.hqx  Sequence entry with sound
     98072 Jun 26 22:00 seqspeak2.hqx  by K. Conover
     30110 Jun 26 22:00 seqspeak3.hqx
    653681 Jun 26 22:24 internet-tour.hqx   A tour of the Internet
      6808 Jun 26 22:24 internet-tour.readme  readme for above
      9073 Jun 26 22:52 mse.hqx Hypercard 2.0 stak for up to 6-seq
                                align & ed 



UNIX

    242 Jun 26 20:22 gde.readme  Genetic Data Environment by S. Smith, readme
 185961 Jun 26 20:21 gde1.0.uaa  version 1.0 tar  file
 186000 Jun 26 20:21 gde1.0.uab  
   9064 Jun 26 20:21 gde1.0.uac
 131874 Jun 26 20:21 gdeps.uue   uuencoded, compress postscript doc file
 185965 Jun 26 20:21 gdesrc.uaa   complete source code for GDE
 186000 Jun 26 20:21 gdesrc.uab    
  21980 Jun 26 20:21 gdesrc.uac
  27815 Jun 26 20:23 gdetxt.uue  uuencoded text file of ps doc file
  92963 Jun 26 20:24 pima.uaa    Randy Smith's Pattern Induced Multiple 
  93000 Jun 26 20:24 pima.uab    Alignment (PIMA) program, version 1.0
  93000 Jun 26 20:24 pima.uac
  93000 Jun 26 20:24 pima.uad
  93000 Jun 26 20:24 pima.uae
  93000 Jun 26 20:24 pima.uaf
  93000 Jun 26 20:24 pima.uag
  33926 Jun 26 20:24 pima.uah
  70177 Jun 26 22:29 overseer.uue  Nucleic acid sequence analysis


DOS

   91915 Jun 26 21:56 cutcost.uaa    New version. Estimate cost of restiction
   14568 Jun 26 21:56 cutcost.uab    enzyme use. C.G. Meinhof
   91918 Jun 26 21:56 prograph.uaa   New version of Prograph, protein
   91921 Jun 26 21:56 prograph.uab   sequence analysis package by
   91921 Jun 26 21:56 prograph.uac   K. Hoffman
   91921 Jun 26 21:56 prograph.uad
   25839 Jun 26 21:56 prograph.uae
   95068 Jun 26 22:14 dnaclone.uaa  Revised DNACLONE, clone
   95071 Jun 26 22:14 dnaclone.uab  and strain management
   85386 Jun 26 22:14 dnaclone.uac
   88005 Apr 23  1990 dnaclone.uue



To get started with the UH Gene-Server send the word
        HELP
to 
        gene-server at bchs.uh.edu
or
        gene-server%bchs.uh.edu at CUNYVM
from BITNET.


Briefly, to retrieve any file use the command (for example)
        send unix pima.uaa pima.uab pima.uac
and you can subsitute "dos", "vms", or "mac" for "unix" in the above.


These files will be appearing on the EMBL, FUNET, and IUBIO servers
soon.


Questions will be answered as time permits.

dan
-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison at uh.edu/DAVISON at UHOU
Disclaimer: As always, I speak only for myself, and, usually, only to
myself.






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