From owner-acedb@net.bio.net Tue Aug 03 23:00:00 1993 Path: biosci!FRODO.MGH.HARVARD.EDU!CHERRY From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: ACEDB data update 1-15 to 1-21 and code 1-10 Message-ID: <930803202041.20207cb5@Frodo.MGH.Harvard.EDU> Date: 4 Aug 93 00:20:41 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 191 ACEDB data update 1-15 to 1-21 and code 1-10 -------------------------------------------- We are sending this list to all those who have asked to be on our mailing lists, plus all those who have installed ACEDB using the automatic INSTALL script. We have eliminated all exact duplicates, but some of you may have received more than one copy, in which case please excuse us. This is a major data release for the C. elegans database. There are also a number of code improvements since 1_9, but we are planning a more significant code release for the next release. Installation ------------ Ftp the correct tar.Z files and our INSTALL script in the ACEDB main directory and type INSTALL. The details are explained at the end of this letter. NEW DATA: --------- We know that we have let the C elegans database run nearly 6 months out of date. We apologize for not distributing data regularly, and have now a lot of new data, including the new CGC genetic map and the seuqencing project cosmids as at the worm meeting. The files in this update are compatible with the previous versions of ACEDB. In order to make the new genetic map, we have worked in Cambridge with a slightly different data format that allows us to represent properly the map data that was sent in earlier this year. We plan to make a new release 2-1 in the next month or two which will use the new data structures. There 7 new update files. 1-15 new genetic map, including estimated accuracies new genetic map data, in old form (see above) new gene data, and gene names physical map 28/6/93 bibliography up to around March 1993 gazette and worm meeting titles and authors up to wm93 changes to other minor classes 1-16 text for all gazette articles up to wbg12.1 (Setember 1991), (thanks to WCS for allowing us to take this data) 1-17 new DNA sequences, including all the cosmids referred to at the worm meeting. 1-18, 1-19, 1-20, 1-21 annotations for sequences The gazette article text is stored under the "Abstract" tag. You can search it all for any component word by setting the "Long Search" option on the main window before starting a text search. This will take a little longer than a standard text search, since the abstracts must be read in from disk. When loading this data you will be asked what size to increase the database to. Reply 90000 (ninety thousand). This takes 90Mb of disk space. We realise that the sequence annotations are very bulky. Most of the reason is that we are storing the complete results of a BLASTX database search for all the cosmids and cdna sequences. This includes the name and title of all matching protein sequences, as well as scores and offsets. We plan to change this structure before the next release, which will shrink the size of the whole database significantly. NEW PORTS: ---------- Acedb has now been ported several new Unix platforms, Sun-Solaris, HP, PC-486 running LINUX, DEC-alpha, Convex etc. The complete list is in wmake directory. It becomes however impossible to test everything on every machine, so, in case of problem, please contact mieg@kaa.cnrs-mop.fr NEW CODE: --------- The code has evolved in several directions. -Fonts and Printer: You can now choose your fonts and drive a color laser printer by editing the self documented files wspec/xfonts.wrm and wspec/psfonts.wrm -Subclass mechanism: You can construct subclasses, which can be used in queries and from the main menu, by editing wspec/subclasses.wrm -Queries: You can now ask for say all authors with first letter m to z by typing '> m' (greater than m) in the main window. You can also search the items in the LongText class by using the 'Long Search' button. In addition 2 new interfaces, contributed by Gary Aochi of LBL-Berkeley, will help you retrieve data. 'Query by examples' follows a simple 'fill-the-blanks' paradigm. It is available from the main menu. Query builder helps you write complex queries, it is available as a button in the query window. -Tables: Table maker, available from the main menu, is a relatively friendly interface that lets you export data as relational tables compatible with other systems like Sybase or Lotus-1-2-3. In addition, you can register some table definitions with some classes in wspec/table.menu.wrm and they are then available as a button in text displays of the objects of that class. -Server clients: A server client architecture is being developed for acedb. At present it only runs in non graphic mode. It can however be very useful to import and export data in and out of acedb in batch mode. The export supports several formats: fasta, ace, and a user defined format which allows you to interspace your text with exported data (see wdoc/client.report.example). The binaries for the server client architecture are not ditributed, you must recompile them or contact us. -Metadata: If you are interested in acedb for other organisms than the nematode, John McCarthy and his group at LBL is working on an online help system on the significance and use of the tags and models of acedb. This code is not part of the present release, but may be of interest to you. -Genetic map display: The presentation of the genetic map in this release is nearly exactly the same as in the previous release. As explained above, a modified display will be released in the future, that will not be compatible with the present data model. Developers will have the choice of keeping the older code or reformatting their data in the newer form. They should contact us now for a prerelease of the new code. -Sequence display: The same is true to a lesser extent of the feature map that presents the dna sequence and features. However in this case, the new data model is rather a simplification of the older one. The reformatting of the data is easy and the present and future code are nearly identical. -Restriction analysis: Restriction analysis of known sequences, available from DNA on the main menu or Analysis at the end of the fmap menu has been improved and can also be used to locate pcr-primers on your own sequences. -Sequence fetch: An interface to external protein databases has been written by Erik Sonnhammer at the Sanger Centre. When you look at a sequence, blastx homologies are displayed as vertical blue rectangle. These support a sub-menu that says "Fetch" and "Show Align". You select it with the right mouse button. Fetch retrieves the whole entry from an external database, and displays it in text form in an acedb window. Align retrieves the sequences and displays a multiple alignment to your translated DNA sequence. Both require an external program in directory $ACEDB/wscripts called "fetch" which acts as follows: Usage: fetch -options Options: -B Choose other database [SW|PIR|EMBL] -q Only the sequence (on one line - used by align) Note that this is not quite the same as the GCG fetch command (unfortunately). The program that we use requires EMBL CDROM style indices, as used by the Staden package. Source code for this version is avilable in fetch.tar.Z from the acedb directory at the standard ftp sites. ----------------------------------------------------------------- Instructions for obtaining updates/the whole thing All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb cele.mrc-lmb.cam.ac.uk (131.11.84.1) in England, in pub/acedb ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp 193.49.104.10 login: anonymous password 'whatever you want' cd pub/acedb binary mget * get README y/n answer yes etc .. .. From owner-acedb@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!cs.utexas.edu!swrinde!network.ucsd.edu!news.cerf.net!pagesat!decwrl!concert!duke!news.duke.edu!bio3.acpub.duke.edu!glh From: glh@bio3.acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: BUG in 1-10? HELP!!! Message-ID: <18680@news.duke.edu> Date: 5 Aug 93 15:35:53 GMT Sender: news@news.duke.edu Reply-To: glh@bio3.acpub.duke.edu (Geoff Hughes) Lines: 30 Nntp-Posting-Host: bio3.acpub.duke.edu Hello out there! First, let me say thanks to all those who attended the ACeDB conference in Boston- from my perspective, it was quite helpful. Special thanks to Richard, Mike, Sam and everyone who gave a presentation. I have run into a problem while converting from 1-9 to 1-10 and was wondering if anyone had had a similar problem and/or a fix. After adding tags to the tags.wrm file for our models, I tried to startup the database and got the following error: !! FATAL ERROR 0: Tag Plasmid = 2501 tries to overwrite tag (NULL KEY) I tried to fix this by changing the tag number, and then commenting out the tag, but then the error was caused by the next tag on our list, which made me think that there might be some sort of recompilation bug. If you have any ideas, suggestions, or fixes, please e-mail me (or post) at glh@acpub.duke.edu I will post a summary after I fix the bug. Thanks, Geoff Hughes From owner-acedb@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!swrinde!emory!emoryu1!emoryu1.cc.emory.edu From: bcresas@emoryu1.cc.emory.edu (Scott Sammons) Newsgroups: bionet.software.acedb Subject: Solaris acedb Message-ID: <4179@emoryu1.cc.emory.edu> Date: 5 Aug 93 12:46:32 GMT Sender: news@emory.edu Reply-To: bcresas@emoryu1.cc.emory.edu Organization: Emory University (BIMCORE) Lines: 12 Nntp-Posting-Host: emoryu1.cc.emory.edu Recently, there was a posting about a Solaris version of acedb. The note mentioned that it was at ncbi.nlm.nih.gov in the repository/acedb directory. I just tried to find it there with no luck. Has it has pulled? Does anyone know the whereabouts? -Scott ============================================================================== | Scott A. Sammons (404) 727-2780 | | Emory University FAX: (404) 727-3659 | | Biomolecular Computing Resource Internet: bcresas@unix.cc.emory.edu | | 3025 Rollins Research Center | | Atlanta, GA 30322 | ============================================================================== From owner-acedb@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!sdd.hp.com!network.ucsd.edu!news.cerf.net!pagesat!decwrl!usenet.coe.montana.edu!netnews.nwnet.net!news.u.washington.edu!poplar1!cgr From: cgr@poplar1.cfr.washington.edu (cgr@poplar1.cfr.washington.edu) Newsgroups: bionet.software.acedb Subject: Re: Solaris acedb Message-ID: <23rj6k$872@news.u.washington.edu> Date: 5 Aug 93 18:23:16 GMT References: <4179@emoryu1.cc.emory.edu> Reply-To: cgr@poplar1.cfr.washington.edu Organization: University of Washington Lines: 27 NNTP-Posting-Host: poplar1.cfr.washington.edu In article 4179@emoryu1.cc.emory.edu, bcresas@emoryu1.cc.emory.edu (Scott Sammons) writes: >Recently, there was a posting about a Solaris version of acedb. The note mentioned >that it was at ncbi.nlm.nih.gov in the repository/acedb directory. I just tried >to find it there with no luck. Has it has pulled? Does anyone know the whereabouts? > >-Scott >============================================================================== >| Scott A. Sammons (404) 727-2780 | >| Emory University FAX: (404) 727-3659 | >| Biomolecular Computing Resource Internet: bcresas@unix.cc.emory.edu | >| 3025 Rollins Research Center | >| Atlanta, GA 30322 | >============================================================================== i recently got some e-mail from N.STOKER@lshtm.ac.uk (Neil Stoker) with this question. the original solaris port (dirty as it is) can be found via anonymous ftp at poplar1.cfr.washington.edu in the directory /pub/acedb. i don't know why it is no longer at ncpi.nlm.nih.gov poplar1.cfr.washington.edu has been down the last week for repair. it is now back in operation. i apologize for any inconvenience. --- carl g. riches college of forest resources internet: cgr@poplar1.cfr.washington.edu university of washington ar-10 voice: 206-543-2764 seattle, wa 98195 fax: 206-543-3254 From owner-acedb@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!sdd.hp.com!network.ucsd.edu!news.cerf.net!pagesat!decwrl!concert!duke!news.duke.edu!bio3.acpub.duke.edu!glh From: glh@bio3.acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: Re: BUG in 1-10? HELP!!! Message-ID: <18686@news.duke.edu> Date: 5 Aug 93 16:29:27 GMT References: <18680@news.duke.edu> Sender: news@news.duke.edu Reply-To: glh@bio3.acpub.duke.edu (Geoff Hughes) Lines: 13 Nntp-Posting-Host: bio3.acpub.duke.edu Much frustration and a little bit of foolishness later, I discovered that adding my tags to the bottom of tags.wrm was a BAD idea, since my tags were numbered lower than the last tags in the file. Simple fix, but it wasn't immediately obvious. That's it! Geoff From owner-acedb@net.bio.net Wed Aug 04 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!magnesium.club.cc.cmu.edu!news.mic.ucla.edu!library.ucla.edu!agate!headwall.Stanford.EDU!nntp.Stanford.EDU!cycle.Stanford.EDU!cherry From: cherry@cycle.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: ACEDB group archives Message-ID: <1993Aug5.053636.14192@leland.Stanford.EDU> Date: 5 Aug 93 05:36:36 GMT Sender: news@leland.Stanford.EDU (Mr News) Organization: Stanford Yeast Genome Project Lines: 49 Archives of the ACEDB BioSci messages are available via anonymous ftp and gopher from net.bio.net. You can use gopher to retrieve messages presented by their Subject. For example using "gopher net.bio.net": --> 11. ACEDB/ then 1. 9307/ 2. 9308/ --> 3. current/ then 1. IMPORTANT BIOSCI INFORMATION. --> 2. ACEDB Workshop Participant List. 3. ACEDB data update 1-15 to 1-21 and code 1-10. The ACEDB messages are searchable via gopher using the following link: Name=ACEDB BioSci Electronic Conference Type=7 Path=7/.index/acedb-biosci Host=genome.stanford.edu Port=70 One path to this link is via "gopher genome.stanford.edu": 2. Help Searching the "" database. --> 3. Other Information/ 4. Saccharomyces Genome then 2. FTP Archives for Molecular Biology/ --> 3. Global Biological Information Servers/ 4. Global Biological Information Servers by Topic/ then 1. AAtDB, An Arabidopsis thaliana Database (1-4) --> 2. ACEDB BioSci Electronic Conference 3. ACEDB, A Caenorhabditis elegans Database (1-14) -- J. Michael Cherry Project Manager, Yeast Genome Database Stanford Genome Sequencing Center, Department of Genetics Stanford University School of Medicine, Stanford, CA 94305-5120 Voice: 415-723-7541 FAX: 415-723-7016 Internet: cherry@genome.stanford.edu From owner-acedb@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!uwm.edu!vixen.cso.uiuc.edu!moe.ksu.ksu.edu!kuhub.cc.ukans.edu!husc-news.harvard.edu!hsdndev!nmr-z!Frodo.MGH.Harvard.EDU!CHERRY From: cherry@Frodo.MGH.Harvard.EDU Newsgroups: bionet.software.acedb Subject: Re: Solaris acedb Message-ID: <1993Aug6.001838.25160@nmr-z.mgh.harvard.edu> Date: 6 Aug 93 00:18:38 GMT References: <4179@emoryu1.cc.emory.edu> Sender: usenet@nmr-z.mgh.harvard.edu (User for USENET news postings) Reply-To: cherry@Frodo.MGH.Harvard.EDU Organization: Molecular Biology, Massachusetts General Hospital Lines: 14 Nntp-Posting-Host: frodo.mgh.harvard.edu In article <4179@emoryu1.cc.emory.edu>, bcresas@emoryu1.cc.emory.edu (Scott Sammons) writes: >Recently, there was a posting about a Solaris version of acedb. The note mentioned >that it was at ncbi.nlm.nih.gov in the repository/acedb directory. I just tried >to find it there with no luck. Has it has pulled? Does anyone know the whereabouts? > The previously announced binary for Solaris was the 1-9 version of ACEDB. Since the current version is 1-10 the old bin tar file was removed. I've been able to compile the 1-10 code on Solaris without any problems but there seems to be some problem that Jean is currently looking into. Hopefully within a few days a binary for Solaris 2.2 will be available on ncbi.nlm.nih.gov. Mike From owner-acedb@net.bio.net Thu Aug 05 23:00:00 1993 Path: biosci!agate!boulder!boulder!dweaver From: dweaver@boulder.Colorado.EDU (Daniel Weaver) Newsgroups: bionet.software.acedb Subject: 1-14 acedb error Summary: syDf1 placed on the wrong chromosome Keywords: chromosome V Message-ID: Date: 6 Aug 93 21:16:52 GMT Sender: news@colorado.edu (The Daily Planet) Organization: University of Colorado, Boulder Lines: 9 Nntp-Posting-Host: beagle.colorado.edu To any and all who are using release 1-14 (and possibly earlier releases, I don't know): I've run into an error in the placement of syDf1 on the genetic map. It comes up on chromosome V at coordinates -4.5 -12.7, when it's real location is on chromosome X. This problem seems to be cleared up on later releases and I have talked to Richard Durbin about it. Just thought I'd pass the word to any other interested parties. Daniel Weaver From owner-acedb@net.bio.net Sat Aug 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!headwall.Stanford.EDU!nntp.Stanford.EDU!cycle.Stanford.EDU!cherry From: cherry@cycle.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: ACEDB Developer's archive Message-ID: <1993Aug8.061956.22456@leland.Stanford.EDU> Date: 8 Aug 93 06:19:56 GMT Sender: news@leland.Stanford.EDU (Mr News) Organization: Stanford Yeast Genome Project Lines: 40 There was a lot of talk at the ACEDB Workshop in Boston about sharing our notes, writtings, source code and models. (Actually there was the same talk last year, but lets be positive.) I've setup the archive to be accessed via anonymous ftp and gopher. For anonymous ftp use the hostname weeds.mgh.harvard.edu look in the acedb_dev directory. If you wish to contribute you can put files in the incoming directory. Please send me a message that you have put something in that directory then I will move it out for general access. For gopher you can connect to weeds.mgh.harvard.edu and ... --> 8. FTP Archives for Molecular Biology/ then --> 3. ACEDB Developer's archive/ I have added my GenBank-to-Ace and BLAST-to-Ace converted to the utility directory. However, I haven't finished the read.me files yet. The "ACEDB, A tool for biological information" document that Sam Cartinhour and I wrote for an Academic Press manual is in the doc directory. Finally I've included the list of names and addresses collected from the participants of the ACEDB Workshop to the workshop directory. Please help us all and give your workshop notes, utilities or whatever might be interesting to just one other person. I'll continue to add items from the AAtDB project to the archive. Mike -- J. Michael Cherry Project Manager, Yeast Genome Database Stanford Genome Sequencing Center, Department of Genetics Stanford University School of Medicine, Stanford, CA 94305-5120 Voice: 415-723-7541 FAX: 415-723-7016 Internet: cherry@genome.stanford.edu From owner-acedb@net.bio.net Thu Aug 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!news.univie.ac.at!alijku11!aci.cvut.cz!rhino.cis.vutbr.cz!rhino.cis.vutbr.cz!not-for-mail From: jbowyer@rhino.cis.vutbr.cz (Bowyer Jeff) Newsgroups: comp.os.msdos.programmer,alt.netgames.bolo,alt.security,comp.sys.sun.misc,alt.video.games.reviews,bionet.software.acedb,bionet.so Subject: International Software Message-ID: <24d8ba$lhh@rhino.cis.vutbr.cz> Date: 12 Aug 93 11:08:26 GMT Organization: Technical University of Brno, Czech Republic Lines: 50 Xref: biosci comp.os.msdos.programmer:13425 alt.netgames.bolo:3118 alt.security:3751 comp.sys.sun.misc:7659 alt.video.games.reviews:14 bionet.software.acedb:63 X-Newsreader: TIN [version 1.2 PL1] Please share your expertise with our mailing list. INSOFT-L on LISTSERV@CIS.VUTBR.CZ Internationalization of Software Discussion List Internationalization of software relates to two subjects: 1. Software that is written so a user can easily change the language of the interface; 2. Versions of software, such as Czech WordPerfect, whose interface language differs from the original product. Topics discussed on this list include: -- Techniques for developing new software -- Techniques for converting existing software -- Internationalization tools -- Announcements of internationalized public domain software -- Announcements of foreign-language versions of commercial software -- Calls for papers -- Conference announcements -- References to documentation related to the internationalization of software This list is moderated. To subscribe to this list, send an electronic mail message to LISTSERV@CIS.VUTBR.CZ with the body containing the command: SUB INSOFT-L Yourfirstname Yourlastname Owner: Center for Computing and Information Services Technical University of Brno Udolni 19, 602 00 BRNO Czech Republic INSOFT-L-REQUEST@CIS.VUTBR.CZ From owner-acedb@net.bio.net Sun Aug 15 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!wupost!howland.reston.ans.net!agate!headwall.Stanford.EDU!nntp.Stanford.EDU!genome.Stanford.EDU!cherry From: cherry@genome.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Physical Mapping Projects and ACEDB Message-ID: <1993Aug16.125011.1202@leland.Stanford.EDU> Date: 16 Aug 93 12:50:11 GMT Sender: news@leland.Stanford.EDU (Mr News) Organization: Stanford Yeast Genome Project Lines: 24 Ian Dunham has kindly provided the text and postscript of a chapter that he wrote for an Academic Press book on human genome computing. It is available via anonymous ftp from weeds.mgh.harvard.edu in the acedb_dev/doc directory as the compressed tar file pmap_acedb_chap.tar.Z. The title of the chapter is "PHYSICAL MAPPING PROJECTS AND ACEDB". The authors are: Ian Dunham, Richard Durbin, Jean Thierry-Mieg and David R. Bentley. Ian says, "It's at a fairly basic level - a sort of user's guide with pictures." Thank you Ian for providing this for the ACEDB developer's archive. Ian's info: Paediatric Research Unit, Division of Medical and Molecular Genetics, UMDS, 8th floor Guy's Tower, London Bridge, SE1 9RT, U.K. -- J. Michael Cherry Project Manager, Yeast Genome Database Stanford Genome Sequencing Center, Department of Genetics Stanford University School of Medicine, Stanford, CA 94305-5120 Voice: 415-723-7541 FAX: 415-723-7016 Internet: cherry@genome.stanford.edu From owner-acedb@net.bio.net Sun Aug 22 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!news-feed-1.peachnet.edu!concert!duke!news.duke.edu!chlamy.botany.duke.edu!user From: chlamy@acpub.duke.edu (Elizabeth Harris) Newsgroups: bionet.software.acedb Subject: Thanks, Geoff! Message-ID: Date: 23 Aug 93 15:51:46 GMT Sender: news@news.duke.edu Followup-To: bionet.software.acedb Organization: Duke University Lines: 17 Nntp-Posting-Host: chlamy.botany.duke.edu This is a public thank-you to Geoff Hughes, who has been working for me since May on an NSF-sponsored summer undergraduate research project. Today is his last day before returning to school as a Duke senior. Starting from ground zero, Geoff has created a prototype ACEDB database for Chlamydomonas, and has done a terrific job of it. I can wholeheartedly recommend him as a future employee or graduate student. I'll be taking over at this point to fill in more data before making the database public later in the year. I would also like to acknowledge e-mail assistance from Sam Cartinhour, Richard Durbin, and the other people Geoff has contacted, and once again to thank Sam, Mike Cherry, and the other participants of the Boston workshop for everything you've all done to help us get started. Thank you, everyone! Elizabeth Harris chlamy@acpub.duke.edu From owner-acedb@net.bio.net Mon Aug 23 23:00:00 1993 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Worm Community System Message-ID: <9308241508.AA14580@greengenes.cit.cornell.edu> Date: 24 Aug 93 15:08:19 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 7 The latest issue of Science has an interesting on article on WCS, an integrated database of which ACEDB is apparently one component, similar to Otto Ritter's Integrated Genome Database. Does anyone know how it's put together? e.g. is it using Jean's aceserver, or is its frontend actually a modification of ACEDB code, or what? Is it publically accessible for us to look at? - Dave Matthews From owner-acedb@net.bio.net Mon Aug 23 23:00:00 1993 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: WCS reference Message-ID: <9308241510.AA14589@greengenes.cit.cornell.edu> Date: 24 Aug 93 15:10:41 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 2 Oops, sloppy data submission there. The article is Science 261:842 '93. - Dave From owner-acedb@net.bio.net Sun Aug 29 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!uknet!pipex!zaphod.crihan.fr!news.univ-rennes1.fr!frmop11.cnusc.fr!barilvm!vms.huji.ac.il!wisipc.weizmann.ac.il! inherit4.weizmann.ac.il! lsprilus From: lsprilus@weizmann.weizmann.ac.il (Jaime Prilusky) Newsgroups: bionet.software.acedb Subject: Searching ".ace" sequences Message-ID: <1993Aug30.085434.20586@wisipc.weizmann.ac.il> Date: 30 Aug 93 08:54:34 GMT Sender: news@wisipc.weizmann.ac.il Organization: Weizmann Institute of Science Lines: 13 X-Xxmessage-Id: X-Xxdate: Mon, 30 Aug 93 11:50:20 GMT X-Useragent: Nuntius v1.1.1d27 Is there a way of searching the acedb/aatdb... sequences "a la GCG's findpatterns"? Is there a mechanism for creating a set of those database sequences that match (accordingly to a given mistmatch value) a provided short pattern? If not present, we migth try to develop such a mechanism. Any suggestions or guidelines are welcomed. Dr Jaime Prilusky, Head Bioinformatics Unit ! LSPRILUS@WEIZMANN.WEIZMANN.AC.IL Weizmann Institute of Science ! fax: 972-8-344113 76100 Rehovot - Israel ! tel: 972-8-343456