New Files and Data on the UH Gene-Server

[Dan Davison]

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As of August 15, the Gene-Server is supported by the National Science
Foundation, grant DIR-9111695.
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*New Software:

All files have been updated against EMBL so the two servers have
the same versions of software. A complete list is appended to this
message.


VMS: MALIGNED, the multiple sequence alignment editor for VMS by Steve Clark,
is revised and available as MALIGNED.UUE. You will need VMS ZOO and
UUDECODE to decode and unpack the file. Both are on the server.
To receive MALIGNED, send the command SEND VMS MALIGNED.UUE to the
gene-server (see the instructions at the end of this message) or 
retrieve it via anonymous FTP to menudo.uh.edu, 129.7.1.6, in 
~ftp/pub/gene-server/vms/maligned.uue

MAC: GBSEARCH.HQX, a HyperCard stak for using the GenBank BLAST server,
is available from the IUBIO archive and via e-mail from the Gene-Server,
SEND MAC GBSEARCH.HQX


*CORRECTION: NSEQTOOL is a Unix program and has been removed from the DOS area.


*DATABASE FILES UPDATES

NOTE: GenBank release 68 is available on Gene-Server, although the
index file thinks it's release 67. That will be fixed in a
the next version of the server software. GenBank  on the
Gene-Server is current though 9/9/91.

PIR Release 29 is available for FTP and by Sunday AM will be available
for e-mail retrieval. To get started send the command SEND PIR-HELP to the
gene-server address, given below.

REBASE files, the Roberts Restriction enzyme database, is available
as RenzData and RenzRefs, respectively (SEND RENZDATA or SEND RENZREFS).




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Obtaining files from the Gene-Server


To get started, send the message
        HELP
via e-mail to
        gene-server at bchs.uh.edu
or
        gene-server%bchs.uh.edu at CUNYVM
from BITNET.

To retrieve a specific file you use the form:
        SEND <area> <file>

where <area> is LOCUS, ACCESSION, DOS, MAC, UNIX, or PIR-ENTRY,
and <file> is one of the file names given in this message or the word
"INDEX" (for software only:e.g SEND DOS INDEX)
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Other files updated or added:

VMS:
  91151 Sep 13 13:30 align_x.uaa Argos et. al (JMB 193:385 1987)
  91154 Sep 13 13:30 align_x.uab  dot matrix/DECWINDOWS
  91154 Sep 13 13:30 align_x.uac  sequence comparison
  91155 Sep 13 13:30 align_x.uad
  91155 Sep 13 13:30 align_x.uae
  88102 Sep 13 13:31 align_x.uaf
  91153 Sep 13 13:31 aligned.uaa 
  29393 Sep 13 13:31 amphi.uue  Jaehnig's memb. prot. str. pred.
  91154 Sep 13 13:31 boxshade.uaa  Plot multiple alignments, marking sim.
  52834 Sep 13 13:31 boxshade.uab  residues, by K.Hoffman
  94295 Sep 13 13:31 ckit.uaa   C toolbox for writing seq. ana. pgms.
  94298 Sep 13 13:31 ckit.uab   W. Gilbert
  57355 Sep 13 13:31 ckit.uac  
  91154 Sep 13 13:31 clustalv.uaa Des Higgins' new Clustal version,
  44054 Sep 13 13:31 clustalv.uab Multiple seq. align.
  13760 Sep 13 13:31 fastembl.com DCL shell for FASTA-MAIL access
  91150 Sep 13 13:31 filter.uaa Argos et. al (JMB 218:33 1991 and
  91153 Sep 13 13:31 filter.uab  Prot. Eng. 3:565) subopt. prot. seq. align.
  57904 Sep 13 13:31 filter.uac  and motif detection
  94304 Sep 13 13:31 gcgdbase.uaa EMBL ext. to GCG V6 for new EMBL format
  26677 Sep 13 13:31 gcgdbase.uab by P. Rice
  57996 Sep 13 13:31 gcgquick.uab Quicksearch speedup by P. rice
  94303 Sep 13 13:31 gcgquick.uue
  91146 Sep 13 13:31 issc.uaa  UIS version of ALIGN_X
  91148 Sep 13 13:31 issc.uab
  91148 Sep 13 13:31 issc.uac
  91149 Sep 13 13:31 issc.uad
  91148 Sep 13 13:31 issc.uae
  91148 Sep 13 13:31 issc.uaf
  41769 Sep 13 13:31 issc.uag
  23117 Sep 13 13:31 malform.uue POSTSCRIPT printing for MALIGNED output
 134339 Sep 13 14:04 maligned.uue Revised MALIGN, uuencoded .ZOO file
  12947 Sep 13 13:31 nocut.com non-cutter list from GCG MAP output
  58878 Sep 13 13:31 oldzoo.uue Old version (pre-2.0) of ZOO
  46196 Sep 13 13:31 proindex.uue  Generate PROSITE index file
  91155 Sep 13 13:31 prosearch.uaa pattern seaching using PROSITE
  25524 Sep 13 13:31 prosearch.uab  db from EMBL; by L. Kolakowski
  38388 Sep 13 13:31 prositec.uue
  95733 Sep 13 13:32 readseq.uue   D. Gilbert's seq file conversion pgm
  42987 Sep 13 13:32 rst_olap.uue Rest. enz sorting for cohesive ends
  80715 Sep 13 13:32 seqedt.uue  EDT-style sequence editor, W. Gilbert
  91147 Sep 13 13:32 sscan.uaa   Signal Scan, eucaryotic signal detect.
  77570 Sep 13 13:32 sscan.uab    by D. Prestridge
  94303 Sep 13 13:32 statsrch.uaa Db searching with stat. significance
  53924 Sep 13 13:32 statsrch.uab  by R. Mott
  91151 Sep 13 13:32 subform.uaa Pgm to prepare sequence database
  91155 Sep 13 13:32 subform.uab  submission forms, by Spaulding and Kyne
  91154 Sep 13 13:32 subform.uac
  91154 Sep 13 13:32 subform.uad
  91154 Sep 13 13:35 subform.uae
  91154 Sep 13 13:35 subform.uaf
  91154 Sep 13 13:36 subform.uag
  91154 Sep 13 13:36 subform.uah
   2602 Sep 13 13:36 subform.uai
  11370 Sep 13 13:36 tfd2prosite.c TFD db conversion to PROSITE format
  94304 Sep 13 13:36 treealig.uaa  Hein's TreeAlign, 11/90 version
  94306 Sep 13 13:36 treealig.uab  
  94306 Sep 13 13:36 treealig.uac
  59374 Sep 13 13:36 treealig.uad
  18552 Sep 13 13:36 uud.c        UUDECODEr for VMS
  91143 Sep 13 13:36 zoo.uaa      archiving program for VMS
  91146 Sep 13 13:36 zoo.uab
  28058 Sep 13 13:36 zoo.uac

DOS:

 94303 Sep 13 13:24 bigmouth.uaa Sounds, for TypeSeq and DigiSeq
 94306 Sep 13 13:24 bigmouth.uab  by H. Jenson
 48963 Sep 13 13:24 bigmouth.uac
 91153 Sep 13 13:24 clustalv.uaa Higgins' et. al new version of CLUSTAL,
 91156 Sep 13 13:24 clustalv.uab  in C.  
 91156 Sep 13 13:24 clustalv.uac
  6241 Sep 13 13:24 clustalv.uad
 97243 Sep 13 13:24 easyclon.uaa Simulation of cloning with plamid drawing
 47338 Sep 13 13:24 easyclon.uab by E.J. Shillitoe (BioTechniques 10:768 '91
 36949 Sep 13 13:24 mapsrt.uue  Sorts GGG MapSort by no. of cuts and name
 79758 Sep 13 13:24 melprot.uue   prot. sec. str. pred and plot.
 94299 Sep 13 13:24 multalin.uaa  multiple sequence alignment
 30713 Sep 13 13:24 multalin.uab   F. Corpet NAR 16:10881 (1988)
 14202 Sep 13 13:24 subsis.uue    subdir handling for PROSIS or DNASIS(tms)
 11370 Sep 13 13:24 tfd2prosite.c  TFD db to prosite format
 18552 Sep 13 13:24 uud.c       UUDECODE source, use to decode UUEMBL.UUE
  5889 Sep 13 13:24 uudecode.pas ditto
 58539 Sep 13 13:24 uuembl.uue ONLY uudecoder to use on Gene-Server/EMBL files

UNIX:

  94299 Sep 13 13:26 blast.uaa Very fast database search, by Myers et. al
  94300 Sep 13 13:26 blast.uab  JMB 215:403 1990
  20323 Sep 13 13:26 blast.uac  requires DFA and LIBNCBI, below
  91155 Sep 13 13:26 clustalv.uaa Higgins' et al. multiple sequence
  30012 Sep 13 13:26 clustalv.uab  alignment CABIOS, in press
  94296 Sep 13 13:26 dfa.uaa    For use with BLAST,
  35418 Sep 13 13:26 dfa.uab      required
  91151 Sep 13 13:26 filter.uaa  Suboptimal align and motif finder
  91152 Sep 13 13:26 filter.uab  by Argos et al., JMB 218:33
  52355 Sep 13 13:26 filter.uac
  91148 Sep 13 13:26 issc.uaa  Sequence comparison pkg. by Argos et. al,
  91149 Sep 13 13:26 issc.uab   JMB 193:385
  91149 Sep 13 13:26 issc.uac
  91148 Sep 13 13:27 issc.uad
  91149 Sep 13 13:27 issc.uae
  91148 Sep 13 13:27 issc.uaf
  88993 Sep 13 13:27 issc.uag
  94303 Sep 13 13:27 libncbi.uaa  For use with BLAST,
  26018 Sep 13 13:27 libncbi.uab   required.
  20613 Sep 13 13:27 mfasta.shar  Shell script for using MAIL-FASTA servers
  69437 Sep 13 13:27 overseer.uue  Pkg for searching na databases
  91149 Sep 13 13:27 sscan.uaa  Signal scan CABIOS 7:203
  25650 Sep 13 13:27 sscan.uab  by D. Prestridge
  11371 Sep 13 13:27 tfd2prosite.c TFD to Prosite format
  94306 Sep 13 13:27 treealig.uaa  Hein TreeAlign multiple sequence
  94307 Sep 13 13:27 treealig.uab   alignment and phylogeny program,
  94306 Sep 13 13:27 treealig.uac   11/90 version
  26106 Sep 13 13:27 treealig.uad
  18552 Sep 13 13:27 uud.c      source for uudecoder

Mac:
  97223 Sep 13 13:21 cheminventory1.hqx  Chemical inventory tracking
  97307 Sep 13 13:21 cheminventory2.hqx  by D. Swartling, requires HyperCard
  51406 Sep 13 13:21 cheminventory3.hqx  2.0
  97223 Sep 13 13:21 clustalv1.hqx   Higgins et. al multiple seq.
  66491 Sep 13 13:21 clustalv2.hqx    alignment
  97223 Sep 13 13:21 covariation1.hqx  ID compensating base changes
  19422 Sep 13 13:21 covariation2.hqx   CABIOS 7:391
  97223 Sep 13 13:21 dbconv1.hqx   Line-oriented db to tab-delim. format
  46003 Sep 13 13:21 dbconv2.hqx
  97223 Sep 13 13:21 embl-search1.hqx Entry retrieval from EMBL CD-ROM
  47846 Sep 13 13:21 embl-search2.hqx
 211572 Sep 13 14:43 gbsearch.hqx    Note size! Gilbert's BLAST hypercard pgm
  56146 Sep 13 13:21 maccompress.hqx Mac version of Unix-compat. compress pgm
  97223 Sep 13 13:21 macpattern1.hqx Ver. 1.4 of MacPattern by
  97307 Sep 13 13:21 macpattern2.hqx  R. Fuchs
  35639 Sep 13 13:21 macpattern3.hqx 
  60432 Sep 13 13:21 macreview.1  P. Markewitz' review of Mac mol bio sw
  25330 Sep 13 13:21 macreview.2
  97276 Sep 13 13:21 macreview1.2
  97224 Sep 13 13:21 matmeth1.hqx Mol. bio. protocols, hypercard
  61549 Sep 13 13:21 matmeth2.hqx  2.0 stax
  97223 Sep 13 13:21 minimim1.hqx More protocols, any hypercard
  97308 Sep 13 13:21 minimin2.hqx  version
  19692 Sep 13 13:21 minimim3.hqx 
  23353 Sep 13 13:21 multidna.hqx Edit several seq. simultaneously
  65422 Sep 13 13:21 readseq.hqx  D. Gilbert's seq. file format conversion
  97224 Sep 13 13:21 refstack1.hqx  Management of reference dbs
  50463 Sep 13 13:21 refstack2.hqx   Hypercard, any version
  97225 Sep 13 13:22 stuffit_161.hqx  Latest StuffIt
  97307 Sep 13 13:23 stuffit_162.hqx
  97307 Sep 13 13:23 stuffit_163.hqx
  97307 Sep 13 13:24 stuffit_164.hqx
  97307 Sep 13 13:24 stuffit_165.hqx
  25524 Sep 13 13:24 stuffit_166.hqx
  97223 Sep 13 13:24 unstuffitdeluxe1.hqx  Latest UnStuffit
  76002 Sep 13 13:24 unstuffitdeluxe2.hqx
  49284 Sep 13 13:24 uud.hqx   uudecoder for Mac


-- 
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

"If the choice had to be made between saving the lives of lawyers or saving
whales, there is little doubt that the overwhelming majority of Americans 
would come down on the side of the whales" Justice Wallach, NY Times 4/3/91

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.