DROSOPHILA INFORMATION NEWSLETTER Volume 9, January 1993 The Drosophila Information Newsletter has been established with the hope of providing a timely forum for informal communication among Drosophila workers. The Newsletter will be published quarterly and distributed electronically, free of charge. We will try to strike a balance between maximizing the useful information included and keeping the format short; priority will be given to genetic and technical information. Brevity is essential. If a more lengthy communication is felt to be of value, the material should be summarized and an address made available for interested individuals to request more information. Submitted material will be edited for brevity and arranged into each issue. Research reports, lengthy items that cannot be effectively summarized, and material that requires illustration for clarity should be sent directly to Jim Thompson (THOMPSON@AARDVARK.UCS.UOKNOR.EDU) for publication in DIS. Materials appearing in the Newsletter will be reprinted in DIS. Back issues of DIN are available from FlyBase in the directory flybase/news/din. Material appearing in the Newsletter may be cited unless specifically noted otherwise. Material for publication should be submitted by e-mail. Figures and photographs cannot be accepted at present. Send technical notes to Carl Thummel and all other material to Kathy Matthews. The e-mail format does not allow special characters to be included in the text. Both superscripts and subscripts have been enclosed in square brackets; the difference should be obvious by context. Bold face, italics, underlining, etc. cannot be retained. Please keep this in mind when preparing submissions. To maintain the original format when printing DIN, use Courier 10cpi font on a standard 8.5" x 11" page with 1" margins. Drosophila Information Newsletter is a trial effort that will only succeed if a broad segment of the community participates. If you have information that would be useful to your colleagues, please take the time to pass it along. The editors: Carl Thummel Kathy Matthews Dept. of Human Genetics Dept. of Biology Eccles Institute - Bldg. 533 Indiana University University of Utah Bloomington, IN 47405 Salt Lake City, UT 84112 812-855-5782; FAX/2577 801-581-2937; FAX/5374 MATTHEWK@INDIANA.EDU CTHUMMEL@HMBGMAIL.MED.UTAH.EDU MATTHEWK@INDIANA.BITNET *** To add your name to the Newsletter distribution list, send one of the following E-mail messages. Via Bitnet -- To: LISTSERV@IUBVM Subject: Message: SUB DIS-L Your real name Via Internet -- To: LISTSERV@IUBVM.UCS.INDIANA.EDU Subject: Message: SUB DIS-L Your real name LISTSERV will extract your user name and node from the E- mail header and add you to the list. Use your Internet address if you have one. You will receive confirmation by E-mail if you have successfully signed on to the list. If you are on the list and do not wish to receive DIN, or you want to remove a defunct address, replace SUB in the above message with UNS. The SUB command can also be used to correct spelling errors in your real name; the new entry will simply replace the old as long as it was sent from the same USERID@NODE address. *** DIN Vol. 9 TABLE OF CONTENTS >Introduction to Drosophila Information Newsletter >How to subscribe to the Newsletter >TABLE OF CONTENTS >ANNOUNCEMENTS >34th Drosophila Conference >REQUESTS FOR MATERIALS >Laboratory stock lists >MATERIALS AVAILABLE >Clones in 60C-D >Libraries >DATABASES/COMPUTING >FlyBase >GENETIC NOTES >New D. sechellia w mutant >New ri allele and its lethal interaction with H >Updates and corrections to the Redbook *** ANNOUNCEMENTS 34th ANNUAL DROSOPHILA RESEARCH CONFERENCE The 1993 fly meetings will be held March 31-April 4, 1993, at the Town and Country Hotel in San Diego, California. The Program Chairman is Gerry Rubin, Life Sciences Annex Building, U. of California, Box 539, Berkeley, CA 94720-0001 (510-643-9945, FAX/9947). The 1993 meeting will have an experimental format that devotes more time to poster presentations and less to slide and plenary sessions. Registration materials can be obtained from the GSA Administrative Office, 9650 Rockville Pike, Bethesda, MD 20814-3998 (301-571-1825, FAX/530-7079). Advance registration deadline is January 27, 1993 (deadline for abstacts has already passed). *** REQUESTS FOR MATERIALS LABORATORY STOCK LISTS WANTED Kathy Matthews, Dept. of Biology, Indiana U., Bloomington, IN 47405-6801, USA. 812-855-5782; FAX/2577; MATTHEWK@INDIANA.EDU. One goal of the FlyBase project (see below) is to simplify the process of identifying potentially useful mutations and then locating stocks that carry those mutations. To this end, we would like to incorporate the stock collections of as many individual laboratories into FlyBase as possible. If you are willing to make your laboratory stock list available, with the understanding that only stocks not available from any of the funded stock centers should be requested from your lab, please contact me. I would like to have computerized lists now for immediate incorporation into FlyBase. Hardcopy lists, if typed, are also useful; I will convert these to machine-readable format as time permits. *** MATERIALS AVAILABLE MOLECULAR CLONING OF GENOMIC DNA FROM THE 60CD REGION Philip J. Gotwals and James W. Fristrom, Dept. of Molecular and Cell Biology, U. of California, Berkeley, CA 94720. In two separate chromosomal walks, we have recovered 230 kilobases of genomic DNA in the chromosomal region uncovered by Df(2R)Px2 (60C1/2-60D9/10). One walk was inititated by jumping from the centromere-distal to the centromere-proximal breakpoint of Df(2R)Px2 using a beta3-tubulin probe (Kimble et al, (1991) Genetics 126:991). We have recovered nearly 100 kilobases of overlapping genomic DNA, primarily carried in cosmids, around the proximal breakpoint. The other walk was initaited from within Df(2R)Px2 using a fragment from the muscarinic acetylcholine receptor (MAR) gene (Shapiro et al., (1989) PNAS 86:9030). We have recovered nearly 130 kilobases of overlapping DNA, housed in both phage and cosmids, surrounding the MAR gene. Anyone interested in obtaining clones from these walks or information regarding the region should contact: Philip J. Gotwals, HHMI, Bld. E17-225, 40 Ames St., MIT, Cambridge, MA 02139, USA. (617) 253-6452; eMAIL: PJGOTWALS@wccf.mit.edu *** COMPILATION OF DROSOPHILA CDNA AND GENOMIC LIBRARIES Carl Thummel, HHMI, 5200 Eccles Institute of Human Genetics, Bldg. 533, U. of Utah, Salt Lake City, UT 84112, USA. 801-581-2937, FAX/5374, CTHUMMEL@HMBGMAIL.MED.UTAH.EDU The following is a listing of Drosophila cDNA and genomic libraries that are currently available and in common use. Please do not request shipment of a library unless you have an immediate use for it - many contributors are concerned about the time and money involved in mailing their libraries. Also, please inquire with local colleagues before requesting a library since many of these libraries are already widely distributed. cDNA LIBRARIES --Nick Brown, Wellcome/CRC Institute, Tennis Court Rd, Cambridge CB2 1QR UK. Phone: 44-223-334128; FAX: 44-223-334089, Email: NB117@MB1.BIO.CAM.AC.UK Vector/Insertion/Complexity/mRNA source pNB40/see ref./3x10[5]/0-4 hr embryo pNB40/see ref./3x10[6]/4-8 hr embryo pNB40/see ref./3x10[5]/8-12 hr embryo pNB40/see ref./1x10[6]/12-24 hr embryo pNB40/see ref./3x10[6]/imaginal discs The Drosophila strain used is an isogenic second chromosome stock: dp cn bw, from the Gelbart lab. Ron Blackman has made a genomic library from this same strain (see below). The vector is a pUC based plasmid with a SP6 promoter at the 5' end of the cDNA and a T7 promoter at the 3' end of the cDNA. The cloning strategy was directional and designed to maximize the number of full- length cDNAs. A useful diagnostic of full-length cDNAs is a non- coding G nucleotide at the 5' end, after the polyC tract; the origin of this nucleotide is, however, unknown. Reference: Brown, N.H., and F.C. Kafatos (1988) Functional cDNA libraries from Drosophila embryos. J. Mol. Biol. 203: 425-437. --Steve Russell, Dept. of Genetics, Univ. of Cambridge, Downing St., Cambridge, CB2 3EH UK. Phone: 44-223-337733, FAX: 44-223-333992, Email: SR120@MOLECULAR-BIOLOGY- 1.BIOLOGY.CAMBRIDGE.AC.UK.BITNET All libraries were made with RNA isolated from Oregon R strain Vector/Insertion/Complexity/mRNA source NM1149/RI/2x10[6]/Male 3rd instar larvae NM1149/RI/6x10[5]/Female 3rd instar larvae NM1149/Directional: RI-HIII/3x10[6]/Adult male heads NM1149/Directional: RI-HIII/1x10[6]/Adult female heads lambda gt11/RI/3x10[5]/Testes --Charles P. Emerson, Jr. or Mary Beth Davis, Biology Dept., Univ. of Virginia, Charlottesville, Virginia, 22901 USA. Phone: 215-728-5283 (Emerson); 215-728-5284 (Davis); FAX: 215-728-2412, Email: emerson@castor.rm.fccc.edu or davis@castor.rm.fccc.edu Vector/Insertion/Complexity/mRNA source/Titer lambda gt10/RI/1x10[6]/late pupae/1x10[10] Blunt-ended cDNA was ligated to EcoRI adaptors, then ligated to EcoRI digested gt10 lambda arms. We have isolated cDNA clones corresponding to MHC isoforms that were lengths of 5940 and 5500 bases. Reference: George, E.L., M.B. Ober, and C.P. Emerson, Jr. (1989) Functional domains of the Drosophila melanogaster muscle myosin heavy-chain isoform are encoded by alternatively spliced exons. Mol. Cell Biol. 9: 2957-2974. --Bruce Hamilton, Division of Biology 216-76, California Institute of Technology, Pasadena, CA, 91125, USA. Phone: 818-356-8353; FAX: 818-449-0756, Email: BAH@citromeo.bitnet or BRUCE@seqvax.caltech.edu Library name/Vector/Insertion/Complexity/mRNA source Head M/lambda EXLX/ApaI-SacI/1.1x10[7]/Oregon R adult heads Head P/lambda EXLX/ApaI-SacI/9x10[6]/Oregon R adult heads Head 1.2/lambda EXLX/ApaI-SacI/2.7x10[6]/Oregon R adult heads Head 2.0/lambda EXLX/ApaI-SacI/1.2x10[6]/Oregon R adult heads Adult/lambda EXLX/ApaI-SacI/>1x10[6]/Oregon R adults 0-24 mojo/lambda EXLX/ApaI-SacI/3.4x10[6]/Can S, 0-24 hr embryos All libraries were cloned directionally into the ApaI-SacI sites of lambda EXLX, as described in ref. 1, with internal restriction sites protected. Lambda EXLX allows in vivo excision of plasmid DNA using a CRE/loxP site-specific recombination system. This vector also allows regulated expression of the insert DNA as a phage T7 gene 10 N-terminal/cDNA fusion protein, under the control of a T7 RNA polymerase promoter (1). The Head 1.2 library was prepared from cDNAs that were size-selected for molecules 1.2 kb or larger by fractionation through an agarose gel. Head 2.0 contains cDNAs that are 2 kb or larger. The cDNA for the Adult library was not size-fractionated. The Adult and mojo libraries were published in ref. 1. The Head M and Head P libraries are unpublished, but I have asked people who use them to refer to ref. 1, since they were constructed in the same way and in the same vector. The two size-selected libraries, Head 1.2 and Head 2.0 were published in ref. 2, which also describes a rapid screening procedure that is very straightforward. References: 1. Palazzolo et al (1990) Gene 88, 25-36. 2. Hamilton et al (1991) Nucl. Acids Res. 19, 1951-1952 --Tom Kornberg, Department of Biochemistry, University of California, San Francisco, CA 94143 USA. Phone: 415-476-8821, FAX: 415-476-3892, Email: tomk@ucsf.cgl.edu Our cDNA libraries were prepared from RNA isolated from Oregon R animals, with the cDNA sequences inserted into the EcoRI site of lambda gt10. Libraries will be shipped by Federal Express. Requests should be accompanied by an appropriate Federal Express Authorization Number. Stage/Library designation/Complexity 0-3 hr embryo/D/300,000 3-12 hr embryo/E/500,000 12-24 hr embryo/F/300,000 1st and 2nd instar/G/200,000 early 3rd instar/H/300,000 late 3rd instar/I/300,000 early pupal/P/300,000 late pupal /Q/300,000 adult male/R/300,000 adult female/S/300,000 Reference: Poole, S., Kauvar, L.M., Drees, B., and Kornberg, T. (1985) The engrailed locus of Drosophila: Structural analysis of an embryonic transcript. Cell 40: 37-43. --Carl S. Thummel, Dept. of Human Genetics, 5200 Eccles Institute, Bldg. 533, University of Utah, Salt Lake City, Utah, 84112 USA. Phone: 801-581-2937, FAX: 801-581-5374, Email: cthummel@hmbgmail.med.utah.edu Vector/Insertion/Complexity/mRNA source lambda gt10/RI/1x10[6]/larval tissues cultured in vitro with cycloheximide + ecdysone lambda ZAP/RI/3x10[5]/late 3rd instar larvae lambda ZAP/RI/4x10[5]/0-1 day prepupae The late third instar cDNA library is available in two size- fractionations that are enriched for either 1-3 kb or 3-6.5 kb cDNAs. Both libraries, however, do contain some smaller inserts. --Peter Tolias, Public Health Research Institute, 455 First Ave., New York, New York, 10016 USA. Phone: 212-578-0815, FAX: 212-578-0804, Email: tolias@wombat.phri.NYU.EDU Vector/Insertion/Complexity/mRNA source lambda gt22A/SalI-NotI/5x10[5]/Canton S ovaries, stages 1-14 This is a cDNA expression library in which the inserts are directionally cloned. A SalI site is present at the 5' end and a NotI site is at the 3' end. --Kai Zinn, Division of Biology, 216-76, Caltech, Pasadena, CA 91125, USA. Phone: 818-356-8352, FAX: 818-449-0679, Email: kai@seqvax.caltech.edu Vector/Insertion/Complexity/mRNA source lambda gt11/EcoRI/1.2x10[6]/Oregon R, 9-12 hr embryos The complexity is an underestimate for larger cDNAs, since it was >5X size-selected for cDNAs larger than 1.8 kb. The complexity could thus be as high as 6x10[6] for these larger inserts. GENOMIC LIBRARIES --Winifred W. Doane, Dept. of Zoology, Arizona State University, Tempe, Arizona 85287-1501 USA. Phone: 602-965-3571, FAX: 602-965-2012, Email: icwwd@asuacad Vector/Insertion/Complexity/DNA source pWE15/BamHI/4x10[4]-1x10[6]/Amy[1,6] mapP[12] strain of D. melanogaster This cosmid vector contains a T3 and T7 promoter on either side of the insertion site, to facilitate the preparation of end- specific probes for chromosomal walking. Reference: Thompson, D.B., and Doane, W.W. (1989) A composite restriction map of the region surrounding the Amylase locus in Drosophila melanogaster. Isozyme Bull. 22: 61-62. --Ron Blackman, Dept. of Cell and Structural Biology, 505 S. Goodwin Ave., Univ. of Illinois, Urbana, Illinois 61801 USA. Phone: 217-333-4459, FAX: 217-244-1648, Email: Ron_Blackman@qms1.life.uiuc.edu Vector/Insertion/Complexity/DNA source lambda EMBL3/BamHI/1x10[6]/Adult Drosophila virilis lambda EMBL3/BamHI/1x10[6]/Embryonic D. melanogaster, see below Both libraries were prepared by MboI partial digestion of the DNA and insertion into the BamHI site of lambda EMBL3. The inserts can be excised by digestion with SalI. Titer is approximately 5x10[9] pfu/ml. The D. melanogaster genomic library is made from animals that are isochromosomal for chromosome 2, dp cn bw. The same strain was used by Nick Brown for his cDNA libraries. --Howard Lipshitz, Division of Biology, 156-29, California Institute of Technology, Pasadena, CA 91125, USA. Phone: 818-356-6446, FAX: 818-564-8709, Email: HDL@ROMEO.CALTECH.EDU Vector/Insertion/Complexity/DNA source Charon 4/EcoRI/6x10[5]/Canton S embryos This is the original Drosophila genomic library from the Maniatis lab. It has been amplified several times but is still useful for most purposes. Reference: Maniatis et al., The isolation of structural genes from libraries of eucaryotic DNA. Cell 15: 687-701. *** DATABASES/COMPUTING FLYBASE - A DROSOPHILA GENETIC DATABASE, RELEASE 9301 The FlyBase Consortium (see below for names and addresses) {Editors' note: The following document has been edited for DIN; section 6 has been omitted, section 8 has been truncated to include only a list of subdirectories and not the files within them, and section 9 has been omitted. The complete document is available from FlyBase as described below.} CONTENTS OF THIS DOCUMENT 1. What is FlyBase 2. The FlyBase Consortium 3. How to contact FlyBase 4. How to obtain FlyBase 5. How to reference FlyBase 6. Differences between printed and computer versions of FlyBase {omitted} 7. Allied databases 8. The structure of FlyBase {truncated} 9. Detailed description of FlyBase {omitted} 10. Future plans for FlyBase 11. Release notes 12. Full addresses of members of the FlyBase Consortium 13. The copyright of FlyBase 13. Acknowledgements 1. WHAT IS FLYBASE FlyBase is a comprehensive database for information on the genetics and biology of Drosophila. It is, or will be (see below), available in several different formats. That released now is a series of flat files in which different data are displayed. FlyBase includes (by permission of Academic Press) all of the material of the Redbook, i.e. The Genome of Drosophila melanogaster by D.L. Lindsley and G. G. Zimm (Academic Press, 1992). A short introduction to FlyBase is to be found in the file flybase/about-flybase.txt. 2. THE FLYBASE CONSORTIUM FlyBase is being built by a Consortium of researchers funded by the National Institutes of Health. This Consortium includes both Drosophila biologists and computer scientists. The Consortium is split between four sites, at Harvard, Cambridge (England), Bloomington and Los Angeles. In addition the Consortium has very close links with the National Center for Biotechnology Information in Washington and with several other workers who provide us with data, either for FlyBase itself or for one of its allied databases. The members of the Consortium are: o Biological Laboratories, Harvard University: William Gelbart (PI) Wayne Rindone Joe Chillemi o Dept. of Genetics, University of Cambridge: Michael Ashburner Rachel Drysdale Aubrey de Grey o Dept. of Biology, Indiana University, Bloomington: Thomas Kaufman Kathy Matthews Don Gilbert o Dept. of Biology, University of California, Los Angeles: John Merriam Beverley Matthews Soon-Young Huh o National Center for Biotechnology Information, NIH, Washington: Carolyn Tolstoshev 3. HOW TO CONTACT FLYBASE FlyBase has established a central e-mail address to which all communications and questions can be sent. This is: o FLYBASE@NUCLEUS.HARVARD.EDU Communications or questions about the Indiana fileserver may be addressed to: o FLYBASE@BIO.INDIANA.EDU We very much welcome corrections and additions to the data in FlyBase, comments about the types of data the we now (or should) make available or about the structure of FlyBase. FlyBase is meant to serve the Drosophila community. Only if we receive some feedback from the community will we know how best to do this. Many of the working papers between members of the FlyBase Consortium are publicly available (see below). The full mail addresses, with telephone and fax numbers and e-mail addresses, of the members of the Consortium are given in the penultimate section of this document. 4. HOW TO OBTAIN FLYBASE FlyBase will be made available in several different ways and formats. These will include direct access to FlyBase servers, versions for stand alone access on different computer platforms, flat files and as printed text (as special issues of Drosophila Information Service, of which DIS 69 was a prototype) (see "Future plans for FlyBase"). In its present form FlyBase is only available as a series of flat files although these can be browsed and queried interactively using publicly available software (see below). The prime archive of FlyBase is maintained on a publicly accessible computer at the Department of Biology, Indiana University (IUBio). The files can be obtained in two ways, either interactively using a Gopher Client (see below) or by anonymous FTP (File Transfer Protocol). A subset of FlyBase files are also kept on several other computers, from where they are available either interactively or by anonymous FTP. If all of this is mysterious to you, contact Don Gilbert, Wayne Rindone or Aubrey de Grey, by mail or phone, for help (see below for contact numbers). WAIS/Gopher: By far the easiest way to access FlyBase is with a Gopher Client. Gopher is a program that runs on a variety of computer platforms (including Macs). To use Gopher you need three things - a suitable computer, access to Internet and a Gopher Client. We cannot help you for the first of these but in view of the plans to make FlyBase available using X-windows software we recommend that, if purchasing, you buy a computer that can support X-windows. For Internet access you must consult your local computer advisors. For those without direct network access there are commercial companies that provide Internet access across telephone lines using modems. The Gopher Client software is available by anonymous ftp from boombox.micro.umn.edu, in the directory /pub/gopher/, or from ftp.bio.indiana.edu, in the directory /util/gopher/. Services on the IUBio Gopher host are also available using WAIS client software. WAIS is the Wide Area Information System. Client software is available for a variety of computer platforms by FTP from IUBio (in the directory /util/wais) and ftp.think.com. It may be convenient, if your main use of Gopher is to search FlyBase, to set up your Gopher client so that access to Indiana is the default. Two of the great advantages of using Gopher are (a) that it allows you to search files interactively and (b) that you need not understand the structure of the FlyBase files. What Gopher provides is an interactive search of the flat files of FlyBase and the ability to transfer all or part of any file back to your home computer. FlyBase is accessible from the Gopher hole at Indiana (IUBio) and most of the files (but not those from the Redbook) are also accessible from the Gopher hole at the Biozentrum in Basel. The link to add to your Gopher server to tunnel to Indiana is: Name=IUBio Biology Archive, Indiana University (experimental) Type=1 Port=70 Path=1/ Host=ftp.bio.indiana.edu The link for the Basel Biozentrum host is: Name=bioftp EMBnet Switzerland (experimental) Type=1 Port=70 Path= Host=bioftp.unibas.ch The WAIS source for the Indiana archive (IUBio) is: (:source :version 3 :ip-address "129.79.224.25" :ip-name "ftp.bio.indiana.edu" :tcp-prot 210 :database-name "INFO" :cost 0.00 :cost-unit none :maintainer "archive@bio.indiana.edu" :description " This WAIS service includes several indexed Biology Information sources, including Genbank nucleic acid sequence databank, Drosophila genetics, Biosci/Bionet network news, and others. File Transfer Protocol (FTP): FlyBase is available by File Transfer Protocol (FTP) from several sources. However only Indiana has the complete set of files. The other sites have most files except those that include the Redbook data. Note that since most of these machines run Unix, the commands and names of directories and files are case sensitive. The FTP servers from which FlyBase is now available are: FTP.BIO.INDIANA.EDU (129.79.224.25). Login with the username anonymous and use your e-mail address as password. FlyBase is in the directory flybase/. NCBI.NLM.NIH.GOV (130.14.20.1). Login with the username anonymous and use your e-mail address as password. FlyBase is in the directory repository/FlyBase. FTP.EMBL-HEIDELBERG.DE (192.54.41.33). Login with the username anonymous and use your e-mail address as the password. FlyBase is in the directory /pub/databases/flybase. SUNBCD.WEIZMANN.AC.IL (132.76.64.79). Login with the username anonymous and your e-mail address as the password. FlyBase is in the directory /pub/databases/flybase. FTP.NIG.AC.JP (133.39.16.66). Login with the username anonymous and your e-mail address as password. FlyBase is in the directory /pub/db/flybase. Once logged in to an FTP server the following commands can be used to obtain one or more FlyBase files onto your own computer: ftp> cd {directory name} (i.e. cd flybase if using IUBio) ftp> get /documents/full.doc ftp> get/genes/loci.txt . et cetera . or ftp> mget *.txt (to retrieve all text files) ftp> quit For those without access to FTP there is a gateway between BITNET/EARN and the FTP part of IP at Princeton. This allows you to make an FTP request by BITNET/EARN mail, the file(s) requested from the remote site being forwarded to you as mail from Princeton. This gateway is known as BITFTP. For information on how you use it send the one-line message HELP to BITFTP@PUCC.BITNET. In brief, this service is used by sending a MAIL message (using BITNET) to BITFTP@PUCC as follows: FTP ftp.bio.indiana.edu NETDATA USER anonymous guest QUIT The files will then be returned to you by e-mail. Netserver: These files are available from the Netserver at EMBL, and if you do not have the facility for FTP this is a way to get them. For general help and a listing of files on the EMBL Netserver send an e-mail message to NETSERV@EMBL- HEIDELBERG.DE with the text HELP FLYBASE. To obtain a particular file send an e-mail message with the text GET FLYBASE:FILENAME to NETSERV@EMBL-HEIDELBERG.DE, where FILENAME is one of the filenames listed above. Direct logon access in the UK: In the UK FlyBase is available on both the SEQNET and HGMP facilities. The SERC SEQNET computing facility at the Daresbury Laboratory (UK.AC.DL.SEQNET) can be directly accessed via JANET. For an account write to Dr. Alan Bleasby, SERC Daresbury Laboratory, Warrington WA4 4AD, Cheshire or send e-mail to AJB@UK.AC.DARESBURY. FlyBase is kept in a directory called /data/flybase. The MRC Human Genome Mapping Project is also accessed via JANET (MENU.CRC.AC.UK). Applications for an account should be sent to The HGMP Resource Centre, Clinical Research Center, Watford Road, Harrow, Middx HA1 3UJ. Access to FlyBase is via the menu. CD ROM: Most of the files of FlyBase (except those of the Redbook) are included in the NCBI Data Repository and EMBL CD- ROMs. These are released periodically and are available from the NCBI Data Repository, National Library of Medicine, Bldg. 38A, Rm 8N-803, NIH, Bethesda, MD 20894 ((1)-301-496-2475) or from the EMBL Data Library, Postfach 10.2209, 6900 Heidelberg, Germany (phone (49)-6221-387258; fax (49)-6221-387519). Dr. Amos Bairoch has made this database available as ascii files on CD ROM. Contact Dr. A. Bairoch, Department of Medical Biochemistry, University of Geneva, Geneva, Switzerland. e-mail: BAIROCH@CMU.UNIGE.CH. 5. HOW TO REFERENCE FLYBASE We suggest FlyBase be referenced in publications in the following manner: FlyBase (1993). A Drosophila Genetic Database. Available from the FTP.BIO.INDIANA.EDU network server. 6. DIFFERENCES BETWEEN PRINTED AND COMPUTER VERSIONS OF FLYBASE [omitted] 7. ALLIED DATABASES It is both undesirable and impossible for literally all data on Drosophila to be kept within FlyBase. However, FlyBase wishes to encourage collaboration between other workers who are building different or more specialized Drosophila databases. For this reason FlyBase has established the concept of allied databases. These databases are explicitly attributed to their authors, who are responsible for the data they include. FlyBase encourages other members of the community to make their databases available associated to FlyBase. In particular, FlyBase encourages other database curators to cross-reference FlyBase to ensure consistency in, for example, gene names and symbols. FlyBase offers help to other curators in both ensuring nomenclatural consistency and in making their databases publicly available through FlyBase. The allied databases now available are listed in the detailed description of FlyBase, below. 8. THE STRUCTURE OF FLYBASE The presently available version of FlyBase is a series of files arranged in a hierarchical structure of directories and subdirectories. An inconvenience of this is that file names can become very long. However, on Unix operating systems, access to a particular directory can be limited by using the cd (change directory) command. The command cd .. (i.e. cd followed by a space and then two periods) will take you up one directory level. Against the disadvantage of cumbersome file names this structure is very logical and easy to maintain. Files are of different types, indicated by the suffixes to their names: .doc an explanatory document, in plain text. .txt a file in plain text, may be data, documentation or other information. .rpt a formatted data file, suitable for viewing by people, in plain text. .rtf a rich-text file, best read with common word processors, but also readable by people, in plain text. .gif an image file (graphic interchange format). Use a gif viewer to see. .ps a postscript image file. Use a postscript viewer or printer. .tar.Z a Unix compressed archive file. Use uncompress and tar to extract. .hqx a Macintosh binhex archive file. Use stuffit to decompress. .zip an MSDos compressed archive file. Use unzip to extract. There now follows the complete structure of the FlyBase files as kept on the IUBio server. The structure may differ when FlyBase is mounted on other computers, but should reflect this structure in a logical way. A detailed description of the contents of each file is given in the next section of this document. Some files have yet to be implemented, but they have been listed here as it is expected that they will be available very soon. If you are using FlyBase through a Gopher client the details of this organization are irrelevant, as you will be presented with the available files by the interactive Gopher menu. flybase/ flybase/redbook flybase/redbook/genes flybase/redbook/lethals flybase/redbook/aberrations flybase/redbook/miscellany flybase/genes flybase/aberrations flybase/maps flybase/function flybase/clones flybase/stocks flybase/stocks/stock-centers flybase/stocks/stock-centers/bloomington flybase/stocks/labs flybase/references flybase/miscellany flybase/sequences flybase/people flybase/news flybase/news/news flybase/news/oldnews flybase/news/din flybase/documents flybase/documents/full.doc {i.e. this document} flybase/working-papers flybase/allied-data 9. DETAILED DESCRIPTION OF FLYBASE {omitted} 10. FUTURE PLANS FOR FLYBASE In this section of the documentation we indicate some of the future directions we are taking with the building of FlyBase. This text is supplemented by the papers in the files of flybase/working-papers. We encourage the fly community to respond to what we are doing - let us know (by e-mail to FLYBASE@NUCLEUS.HARVARD.EDU or by regular mail to any of us) if you think we are not doing something that should be done, or are doing something that should not be done. Only by feedback from the community will we produce a product of the greatest utility to all. As we have explained elsewhere in this document the present release of FlyBase is seen very much as a temporary measure, until the full relational schema has been implemented. The relational schema: FlyBase is being built and will be maintained in a commercial relational database management system called Sybase. The design of the relational schema can be found in a series of files in flybase/working-papers/sybase-*. This schema was designed by Carolyn Tolstoshev. It is not yet stable - that is to say changes to the schema are still being made as a consequence of experience and discussion. The Harvard group are now implementing and testing this schema prior to the importation of data. The data: Any database is only as good as its data and the way these data are interrelated. At present, FlyBase data are available as a series of independent tables with few relationships between them. Not only does this mean that there are major inconsistencies between tables (e.g. a gene may have one symbol in one table but another in a second) but also it means that the user cannot automatically go from e.g. the loci table to a stock table. One of the major tasks that is now being done is to force consistency between tables. 1. The bulk of the genetic data is now in two sets of directories, flybase/redbook - the text material of Lindsley and Zimm, and flybase/genes and flybase/aberrations (with flybase/maps, flybase/function, flybase/references). The Cambridge group is now integrating these two sets of tables into a single structure. This will, in effect, be the replacement of the Redbook. Since science does not stop simply because we are building this database the Cambridge group is also continuously updating the data, by scanning the literature. 2. There are now several different tables of clone data. These are being integrated and continuously updated by the Los Angeles group. This group is also developing software for the graphical display of molecular data. 3. References can now be found in three different sets of tables, those in flybase/redbook, flybase/genes and flybase/clones/clonelist.txt. Not only is there redundancy between these but each set differs in its reference format. The Cambridge group is dealing with this problem by building a single Drosophila reference file. The objective is to have as complete a bibliography on Drosophila biology as possible with all entries in uniform format. The sources of this bibliography are several: the published bibliographies (Morgan et al. 1925, Muller, Herskowitz and some smaller more specialized ones) are being read by an optical character reader; we have concluded a license agreement with MEDLINE giving us a retrospective download from 1966 (the year MEDLINE introduced computer files) with monthly updates from January 1993 (these entries will include abstracts) and Dr. G. Bachli's computer bibliography, which is especially strong on taxonomic and faunistic papers. When these have all been entered, duplicate entries removed and reformatted they will be checked against the large Drosophila offprint collection in Cambridge for errors and omissions. This reference table will serve all of the other tables of FlyBase. Users will be able to recover references from it in a variety of formats (e.g. that used by ENDNOTE). 4. The Bloomington group is working on the problem of stock lists, not only collecting stock lists from other laboratories (see flybase/stocks.doc) but also ensuring a consistency in format, so that all can be seen in a similar way. We hope to publish a recommendation for stock list format, with the hope that others will use it and reduce the problems we have in displaying stock list data. The second major problem with the stock lists is to ensure that they are consistent in the symbols used for genes, alleles, aberrations and insertions. 5. There are now several different files of addresses and/or e- mail addresses. These have been gathered from various sources. The aim is to have a single address file, in a consistent format. This work is being done in Bloomington. 6. The formal description of chromosome aberrations, in a manner suitable for manipulation by computer programs, is a difficult problem. One approach is that discussed in flybase/working- papers/aberration-syntax.txt. We are writing software that will allow efficient searching of the aberration tables for, e.g., breakpoints within a specific chromosome region, and allow the graphical display of aberrant chromosomes. Output: Although FlyBase will be built and maintained in Sybase we expect few to have the skills to use it as such or to have the very considerable cash required for a Sybase operating license. For this reason we are building a number of output products that will make FlyBase available to as wide a community as possible. (The Sybase implementation will be publicly available should any users need it.) 1. The simplest output will be printed text. We have, in pre- Consortium days, experimented with this with a special volume of DIS (DIS 69) compiled by Michael Ashburner and edited (and distributed) by William Gelbart. It is our intention to publish such special issues of DIS whenever the amount of new data warrants. By doing this we will ensure that even those workers who have no access to computers or networks will not be disenfranchised. These issues of DIS will be produced as output from the Sybase tables. 2. The presentation of FlyBase as a series of ascii flat files on computer servers will be maintained. The prime server will be that at IUBio and the Bloomington group will continue to make improvements in access and display of these tables. By far the easiest way to access these files is by using a Gopher client (see "How to obtain FlyBase"). In addition these tables will be distributed, as now, to a number of major servers used by biologists and will be included on the CD-ROMs being distributed by NCBI, EMBL and others. 3. There is now strong interest in the development of software to display databases such as FlyBase interactively using X-windows systems. We are developing such tools for use with FlyBase. We are concentrating our efforts in two ways. The first is to exploit the software tools written at the NCBI for use with their Entrez system. The second is to develop the programs written by Richard Durbin and Jean Thierry-Meig for the C. elegans database - acedb. acdeb is now being modified for Drosophila data in Berkeley and we are collaborating with Suzanna Lewis to make these programs suitable for the display of FlyBase. These implementations of FlyBase will be available from the IUBio server (and probably from other servers), on CD-ROM and perhaps on floppy discs. To make use of them you will need a computer that can implement X-window software (or its equivalent). A color monitor would be a great advantage. 11. RELEASE NOTES Since FlyBase is still kept as a series of independent tables the concept of a "release" or "version" of the database is difficult to apply. However, while this format continues we will signal new releases (as yearmonth) whenever we consider that there has been a sufficient change in data or organization to warrant it. New versions of particular tables may well be released without obvious notice. One way of finding out is to look at the date that a particular file was last modified on IUBio. This can be done by FTP using the dir command in the flybase directory. The last update of a file is automatically displayed by Gopher. The individual document files will be kept up to date and they will indicate any changes in organization or major changes in content. The last update of the .doc files is displayed on the top line of each. Release 9301 of FlyBase is the first by the Consortium. It is released as a temporary measure to make the data that is in FlyBase already available to the community. In large part 9301 is simply a restructuring of data that had been previously available from IUBio and other sources. It includes the tables from the 9209 release of Michael Ashburner (see flybase/news/oldnews/1992.txt). These tables include 5321 loci, 4218 entries in the genetic map, 11940 aberrations and 3120 references. Note that of the 5321 loci, about 800 are not in Lindsley and Zimm (1992). The great majority of the references are also subsequent to Lindsley and Zimm. This release includes tables from the 3/06/1992 release of John Merriam's clone lists. 12. FULL ADDRESSES OF MEMBERS OF THE FLYBASE CONSORTIUM William Gelbart, Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA. Telephone: (1)-617-495-2906; fax: (1)-617-495-9300; e-mail: GELBART@MORGAN.HARVARD.EDU. Wayne Rindone, Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA. Telephone: (1)-617-496-5668; fax: (1)-617-495-9300; e-mail: RINDONE@MORGAN.HARVARD.EDU. Joe Chillemi Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA. Telephone: (1)-617-496-5667; fax: (1)-617-495-9300; e-mail: JOEC@MORGAN.HARVARD.EDU. Michael Ashburner, Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, England. Telephone: (44)-223-333969; fax: (44)-223-333992; e-mail: MA11@GEN.CAM.AC.UK. Rachel Drysdale, Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, England. Telephone: (44)-223-333963; fax: (44)-223-333992; e-mail: RD120@GEN.CAM.AC.UK. Aubrey de Grey, Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, England. Telephone: (44)-223-333963; fax: (44)-223-333992; e-mail: AG24@GEN.CAM.AC.UK. Thomas Kaufman, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA. Telephone (1)-812-855-3033; fax: (1)-812-855-2577; e-mail: KAUFMAN@BIO.INDIANA.EDU. Kathy Matthews, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA. Telephone (1)-812-855-5782; fax: (1)-812-855-2577; e-mail: MATTHEWK@UCS.INDIANA.EDU. Don Gilbert, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA. Telephone (1)-812-855-7807; e-mail: GILBERT@BIO.INDIANA.EDU. John Merriam, Department of Biology, University of California at Los Angeles, Los Angeles, California 90024-1606, USA. Telephone: (1)-310-825-2256; fax: (1)-213-206-3987; e-mail: IBENAPR@OAC.UCLA.EDU. Beverley Matthews, Department of Biology, University of California at Los Angeles, Los Angeles, California 90024-1606. Telephone: (1)-310-825-2256; fax: (1)-213-206- 3987. Soon-Young Huh, Department of Biology, University of California at Los Angeles, Los Angeles, California 90024-1606. Telephone: (1)-310-825-2256; fax: (1)-213-206-3987; e-mail: SHUH@AGSM.UCLA.EDU. Carolyn Tolstoshev, National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA. Telephone: (1)-301-496-2475; fax: (1)-301-480-9241; e-mail: CAROLYN@NCBI.NLM.NIH.GOV. 13. THE COPYRIGHT OF FLYBASE The files containing the text of Lindsley and Zimm (1992) The genome of Drosophila melanogaster are the copyright of Academic Press and are redistributed in FlyBase by their agreement. These files cannot be redistributed by users without the explicit permission of Academic Press. The copyright of FlyBase itself is held by the Genetics Society of America. 14. ACKNOWLEDGMENTS FlyBase is supported by a grant from The National Center for Human Genome Research. In addition support has come from the HGMP Programme of the MRC (London) in the form of both hardware and software. Work in John Merriam's group has been supported by a grant from the National Library of Medicine. The Drosophila Stock Center at Bloomington is supported by NSF's Division of Instrumentation and Resources. We acknowledge the help of Dr. Phyllis Moses (Academic Press) and Dr. D.L. Lindsley in making the Redbook data available to FlyBase. We thank Drs. D.J. Lipman and J. Ostell and the staff at the NCBI in Washington for their help in getting FlyBase launched. We are very grateful to Rainer Fuchs at EMBL, Amos Bairoch in Geneva, Alan Bleasby at Daresbury, Scott Federhen at the NCBI, Yoshihiro Ugawa and Takashi Gojobori at the DDBJ, Martin Bishop at the HGMP and Reinhard Doelz at the Biozentrum for helping to make this database available. Thanks too to John Garavelli (PIR), Rainer Fuchs (EMBL) and Amos Bairoch (Geneva) for help in cross-checking between FlyBase and the Nucleic Acid/Protein databases. We also thank Dr. G. Bachli (Zurich) for a substantial contribution to the bibliographic file. *** GENETIC NOTES A NEW MUTANT OF D. SECHELLIA Isaya Higa and Yoshiaki Fuyama, Dept. of Biology, Tokyo Metropolitan U., Hachioji-Shi, Tokyo 192-03, Japan. 81-426-77-2575, FAX/2559; A910741@JPNTMU00.BITNET. A new white (w) mutant of D. sechellia spontaneously occurred in an iso-female strain originally collected in Plaslin Island, Seychelles in 1986. General features are the same as those of white of D. simulans and white[1] of D. melanogaster. Homozygote fertile and viability normal. Sex-linked and recessive. Does not complement white of D. simulans. *** NEW RADIUS INCOMPLETUS ALLELE AND ITS LETHAL INTERACTION WITH HAIRLESS Petter Portin and Mirja Rantanen, Laboratory of Genetics, Dept. of Biology, U. of Turku, SF-20500 Turku, Finland. SEPNE@SARA.CC.UTU.FI In June 1992 we began to suspect that a spontaneous radius incompletus (ri) mutation had occurred in our Ax[ts1] stock. We mapped this mutation with the aid of cu and es mutations, and found that the new mutation really mapped to the position of ri (3-47.0). Our new mutation failed to complement ri, and consequently it was named ri[92f]. Even earlier we had found that in the cross ri[92f] cu es x H es cd/In(3R)P, spr only non-ebony progenies appeared. Therefore we concluded that the interaction of ri and H is lethal even though both are in a heterozygous condition. *** CORRECTIONS FOR REDBOOK Dan Lindsley and Georgianna Zimm, Dept. of Biology, U. of California, La Jolla, CA 92093. 619-534-3109, FAX/0053. p=page, L=left, R=right p2L, line 12: choromosomes > chromosomes p8R, ABO table footnote: Sander> Sandler p25L, Ama-1: alpha-amanatin> alpha-Amanatin p41R, zen: Location> location p71R, bottom of page: Add entry "bcd:: see ANTC" p100: Add entry "Ubx[16K] X ray Ramey In(3R)79D;89B Ubx" p100: Add entry "Ubx[42T] X ray In(3R)70D;89E Ubx" p100: Add entry "homozygous lethal" to last column of Ubx[130]. p101: Add entry "; T(2;3) " to cytology column and entry "Ubx" to type column of Ubx[A] p109: Add entry "extreme Ubx" to type column of Ubx[U] p109R: Add entry "cel: see l(3)84Ab" p128R: Add entry "cry: see Su(Ste)" p128R: Add entry "crystal: see Su(Ste)" p142L: Add entry "da[12] 7 recessive lethal" p142L: Add entry "da[13] 7 recessive lethal" p142L: Add entry "da[14] 7 recessive lethal" p142L: Add entry "da[15] 7 recessive lethal" p142L: Add entry "da[16] 7 recessive lethal" p142L: Add entry "da[17] 7 recessive lethal" p142L: Add entry "da[18] 7 recessive lethal" p142L: Add entry "da[19] 7 recessive lethal" p142L: Add entry "da[20] 7 recessive lethal" p142L, da table footnote: Add entry "7 = Grigliatti." p142L, da cytology: Change to "Placed in 32A by fine-structure deficiency analysis of region 31A-32A by Grigliatti et al." p183R: E(Sd)> E(SD) p201R, err alleles: Add entry "err[2] - err[4] also isolated." p201R, err cytology: Change to "Placed in 31E by fine-structure deficiency analysis of region 31A-32A." p249R, Gbeta13F location: 2-{54}> 2-{51} p255L: Add entry "Glucose-tasting-defective: see Gtd." p255L: Add entry "Glutamic acid decarboxylase: see Gad." p259R: Add entry "grh, grainy head: see Ntf." p259R: Add entry "groggy: see ggy." p268L, H references: Add entry "Plunkett, 1926, J. Exp. Zool. 46: 181-244." p268L, H references: Add (after "Development") "111: 89-104." p268R, H[17] (in table): Add entry "gamma ray Posakony/Groger" p268R, H[18] (in table): Add entry "gamma ray Posakony/Groger" p268R, H[19] (in table): Add entry "gamma ray Posakony/Groger" p268R, H[20] (in table): Add entry "gamma ray Posakony/Groger" p268R, H[21] (in table): Add entry "gamma ray Posakony/Groger" p268R, H[21] (in table): H[C]> H[C23] p268R, H[22] (in table): Add entry "gamma ray" p268R, H[22] (in table): Bang> Posakony p268R, H[22] (in table): H[C]> H[RP1] p268R, H[26] (in table): Add entry "X ray." p288L, inC alleles: InC[1] - InC[3]> inC[1] - inC[3] p309L (in l(1)2A table): l(1)2Af (bold face)> l(1)2Af (regular) p309L (in l(1)2A table): sta> sta (bold face) p509R, nod references: Genetics (submitted)> Genetics 125:115-27. p555L, pn: awk[K]> awd[K] (appears twice) p555R, pn: awk[K]> awd[K] (appears four times) p570R, qua: Nsslein-> Nusslein (diaeresis over the u) p570R, qua: f2qua[2] - qua[7]> qua[2] - qua[7] (in italics) p621L: Add entry "scabrous> sca" p621L: Add entry "shaven baby> sv" p740R: For the entry unk, see the CYTOGENETIC MAP, p1132. p1067: change figure explanation to "the third row shows the N- banding pattern (provided by Pimpinelli, Bonaccorsi, Dimitri, and Gatti.)." p1068L: Change reference for figure explanation to "(Pimpinelli, Bonaccorsi, Dimitri, and Gatti)." p1069L: Change reference for figure explanation to "(Pimpinelli, Bonaccorsi, Dimitri, and Gatti)." p1069R (upper): Change reference for figure explanation to "(Pimpinelli, Bonaccorsi, Dimitri, and Gatti)." p1069R (lower): Change reference for figure explanation to "(Pimpinelli, Bonaccorsi, Dimitri, and Gatti)." Notes appended to Redbook by attendees at the Philadelphia fly meeting: exo: exocephalon is allelic to phm: phantom (Eberl) mat(2)N mutations are hypomorphic alleles of l(2)31Ei Sryc likely to correspond to wdn (Lepesant) fs(1)A107 renamed brn: braniac (can't read signature) fs(1)1621 renamed snf: simply not fertile (Saltz) Kin: Kinesin should be Khc: Kinesin heavy chain (Saxton) l(1)3Ac renamed trol: troll by Datta and Kandel {not l(1)trol as they suggest} l(3)73Ab will be named soon (Andrew) l(3)85Ee renamed hyd: hyperplastic discs (Shearn) l(3)SG29 renamed md: minidiscs (Shearn) l(3)SG56 renamed qrt: quartet (Shearn) New genes inserted into list by participants: Chc: Clathryn heavy chain dco: discs overgrown (see Developmental Biology 140: 413-429) Gprk1 Gprk2 Pra: Paramyosin rdgC: retinal degeneration C tsh: teashirt A change that we suggest: ms(3)sa should be sa: spermatocyte arrest Symbols used by Ashburner that I prefer over ours: l(1)17Aa through l(1)17Ad instead of l(1)16Fa through l(1)16Fd LanA, LanB, and LanC instead of Lam-A, Lam-B, and Lam-C Pk17C instead of Pk?4 Pk45C instead of Pk?3 Pk53C instead of Pk?7 Pk64F instead of Pk?6 Pk91C instead of Pk?2 Other new synonymy: Pkc2 is the same as inaC sbl mutations are allelic to para ***