From bronze!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!uwm.edu!bionet!UH.EDU!Davison Fri Sep 13 17:49:42 EST 1991
Article: 1981 of bionet.general
Path: bronze!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!uwm.edu!bionet!UH.EDU!Davison
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.general
Subject: New Files and Data on the UH Gene-Server
Message-ID: <199109132207.AA23013@Menudo.UH.EDU>
Date: 13 Sep 91 22:07:15 GMT
Sender: daemon@genbank.bio.net
Distribution: bionet
Lines: 240
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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).
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Obtaining files from the Gene-Server
To get started, send the message
HELP
via e-mail to
gene-server@bchs.uh.edu
or
gene-server%bchs.uh.edu@CUNYVM
from BITNET.
To retrieve a specific file you use the form:
SEND
where is LOCUS, ACCESSION, DOS, MAC, UNIX, or PIR-ENTRY,
and is one of the file names given in this message or the word
"INDEX" (for software only:e.g SEND DOS INDEX)
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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@uh.edu/DAVISON@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.