From owner-embldatabank@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!darwin.sura.net!lhc!ray!dab From: dab@ray.nlm.nih.gov (Dennis Benson) Newsgroups: bionet.molbio.embldatabank Subject: Sequence Data Submissions Message-ID: <1993Sep9.232937.5862@nlm.nih.gov> Date: 9 Sep 93 23:29:37 GMT Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 68 X-Newsreader: Tin 1.1 PL4 -------------------------------------------------------------------------- Sequence Data Submissions to GenBank, EMBL, and DDBJ -------------------------------------------------------------------------- The sequence databases depend on scientists to contribute sequences and associated biological annotation in electronic form. The three databases in the U.S., Europe, and Japan collaborate in collecting and distributing all sequence information received and consequently make available comprehensive collections of DNA and RNA sequence data in the GenBank, EMBL, and DDBJ databases. Researchers are encouraged to submit data to whichever of the three databases is most convenient. The receiving database will transmit the data to the other two. Collectively, the databases will make the sequence information available to scientists throughout the world through computer networks, magnetic tapes, and CD-ROMs. Many editorial policies require submission of sequence data and the issuance of an accession number by the databases as a condition of publication. (At the authors' option, sequence data may be kept confidential until publication.) But even when not required, the inclusion of an accession number in a publication helps users efficiently retrieve the sequence from the databases. To facilitate the submission process, free software (Authorin) for PC and Macintosh computers is available. Contact NCBI for the software at the address below. For assistance with sequence submission, contact the most convenient database: GENBANK: National Center for Biotechnology Information National Library of Medicine Bldg. 38A, Rm. 8N-803 Bethesda, MD 20894 USA +1 (301) 496-2475 Submissions: gb-sub@ncbi.nlm.nih.gov Revisions: update@ncbi.nlm.nih.gov Information: info@ncbi.nlm.nih.gov EMBL Data Library EMBL Postfach 10.2209 Meyerhofstrasse 1 69012 Heidelberg Germany +49 (6221) 387258 Submissions: datasubs@embl-heidelberg.de Revisions: update@embl-heidelberg.de Information: datalib@embl-heidelberg.de DNA Databank of Japan DDBJ National Institute of Genetics Mishima Shizuoka 411 Japan +81 559 75 0771 Submissions: ddbjsub@ddbj.nig.ac.jp Revisions: ddbjupdt@ddbj.nig.ac.jp Information: ddbj@ddbj.nig.ac.jp From owner-embldatabank@net.bio.net Sun Sep 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!news.ans.net!malgudi.oar.net!chemabs!ljc55 From: ljc55@cas.org (Linda J. Carter) Newsgroups: bionet.molbio.embldatabank Subject: PCR primers and hybridization probes Keywords: biosequence database PCR primer and hybridization probe Message-ID: <1993Sep13.172843.20432@cas.org> Date: 13 Sep 93 17:28:43 GMT References: <1993Sep9.232937.5862@nlm.nih.gov> Sender: usenet@cas.org Reply-To: ljc55@cas.org Organization: Chemical Abstracts Service Lines: 28 For those of you interested in PCR primers and hybridization probes I would really appreciate your opinions about their inclusion in biosequence databases. Some of my specific concerns are as follows: 1. Do you feel primers and probes tend to clutter up a nucleic acid database and cause unnecessary retrievals when searching for sequences of much longer length? 2. Because primers and probes are usually designed from known sequence information often already in the database, is it still justifiable to include them as additional entries? 3. What applications of primers and probes should justify their inclusion in a biosequence database, e.g. clinical diagnosis, taxonomy, evolution, gene mapping, or methods? 4. If you were to search for primers and probes in a biosequence database what would be most efficient for you? Would some type of descriptive information be helpful, e.g. their application or their origin? Thank you very much for any thoughts you might have on this subject. Please post your response to ljc55@cas.org From owner-embldatabank@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!festival!castle.ed.ac.uk!sss From: sss@castle.ed.ac.uk (S S Sturrock) Newsgroups: bionet.molbio.embldatabank Subject: Hmmmmmm Message-ID: Date: 14 Sep 93 13:35:18 GMT Sender: news@festival.ed.ac.uk (remote news read deamon) Organization: University of Edinburgh Lines: 54 OK, who wants to claim responsibility for this found in embl35? Note the rather interesting composition :-) ID A01448 standard; DNA; PRO; 397 BP. XX AC A01448; XX DT 29-MAR-1993 (Rel. 35, Created) DT 29-MAR-1993 (Rel. 35, Last updated, Version 1) XX DE E.coli tyrB aminotransferase protein sequence XX KW . XX OS Escherichia coli OC Prokaryota; Bacteria; Gracilicutes; Scotobacteria; OC Facultatively anaerobic rods; Enterobacteriaceae; Escherichia. XX RN [1] RA Primrose S.B., Edwards R.M.; RT "The cloning and utilization of aminotransferase genes."; RL Patent number EP0293514-A/2, 07-DEC-1988. RL G.D. Searle & Co. . XX FH Key Location/Qualifiers FH FT source 1. .397 FT /organism="Escherichia coli" XX SQ Sequence 397 BP; 51 A; 5 C; 30 G; 15 T; 296 other; A01448 Length: 397 September 14, 1993 14:21 Type: N Check: 5412 .. 1 VFQKVDAYAG DPILTLMERF KEDPRSDKVN LSIGLYYNED GIIPQLQAVA 51 EAEARLNAQP HGASLYLPME GLNCYRHAIA PLLFGADHPV LKQQRVATIQ 101 TLGGSGALKV GADFLKRYFP ESGVWVSDPT WENHVAIFAG AGFEVSTYPW 151 YDEATNGVRF NDLLATLKTL PARSIVLLHP CCHNPTGADL TNDQWDAVIE 201 ILKARELIPF LDIAYQGFGA GMEEDAYAIR AIASAGLPAL VSNSFSKIFS 251 LYGERVGGLS VMCEDAEAAG RVLGQLKATV RRNYSSPPNF GAQVVAAVLN 301 DEALKASWLA EVEEMRTRIL AMRQELVKVL STEMPERNFD YLLNQRGMFS 351 YTGLSAAQVD RLREEFGVYL IASGRMCVAG LNTANVQRVA KAFAAVM -- \. That is biological Captain! | Shane Sturrock, BRU, Darwin Building, (}:-( -- Mr Sturrock | University of Edinburgh, Scotland, /' | Untied Kingdom (Split now!) :-) From owner-embldatabank@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!cs.utexas.edu!uunet!pipex!uknet!pavo.csi.cam.ac.uk!nntp-serv.cam.ac.uk!sre From: sre@al.cam.ac.uk (Sean Eddy) Newsgroups: bionet.molbio.embldatabank Subject: Re: Hmmmmmm Message-ID: Date: 14 Sep 93 18:33:53 GMT References: Sender: news@infodev.cam.ac.uk (USENET news) Organization: Laboratory of Molecular Biology, MRC, Cambridge UK Lines: 22 In-Reply-To: sss@castle.ed.ac.uk's message of Tue, 14 Sep 1993 13:35:18 GMT Nntp-Posting-Host: al.mrc-lmb.cam.ac.uk In article sss@castle.ed.ac.uk (S S Sturrock) writes: >OK, who wants to claim responsibility for this found in embl35? >Note the rather interesting composition :-) >ID >A01448 > standard; DNA; PRO; 397 BP. >DE >E.coli tyrB aminotransferase protein sequence That's definitely the best one, but not all. Much less dramatic examples: A01881 - a patent DNA sequence containing an "l" - probably the key to the patent :) A04243 - a patent peptide sequence "aagrripgx" which might slip through some automated protein vs. nucleic acid sequence checkers - looks like DNA except for the p and i Sure did discover how tolerant my software was to unrecognized symbols when we installed EMBL 35 :) -- - Sean Eddy - Laboratory of Molecular Biology, MRC, Cambridge UK - sre@mrc-lmb.cam.ac.uk From owner-embldatabank@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!HERMES.CHPC.UTEXAS.EDU!mwitten From: mwitten@HERMES.CHPC.UTEXAS.EDU Newsgroups: bionet.molbio.embldatabank Subject: CONGRESS: COMPUTATIONAL MEDICINE AND PUBLIC HEALTH (long) Message-ID: <9309141757.AA08600@morpheus.chpc.utexas.edu> Date: 14 Sep 93 17:57:08 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 555 ** NOTE CHANGES IN SUBMISSION AND REGISTRATION DEADLINES ** FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE, PUBLIC HEALTH AND BIOTECHNOLOGY 24-28 April 1994 Hyatt Regency Hotel Austin, Texas ----- (Feel Free To Cross Post This Announcement) ---- 1.0 CONFERENCE OVERVIEW: With increasing frequency, computational sciences are being exploited as a means with which to investigate biomedical processes at all levels of complexity; from molecular to systemic to demographic. Computational instruments are now used, not only as exploratory tools but also as diagnostic and prognostic tools. The appearance of high performance computing environments has, to a great extent, removed the problem of increasing the biological reality of the mathematical models. For the first time in the history of the field, practical biological reality is finally within the grasp of the biomedical modeler. Mathematical complexity is no longer as serious an issue as speeds of computation are now of the order necessary to allow extremely large and complex computational models to be analyzed. Large memory machines are now routinely available. Additionally, high speed, efficient, highly optimized numerical algorithms are under constant development. As these algorithms are understood and improved upon, many of them are transferred from software implementation to an implementation in the hardware itself; thereby further enhancing the available computational speed of current hardware. The purpose of this congress is to bring together a transdisciplinary group of researchers in medicine, public health, computer science, mathematics, nursing, veterinary medicine, ecology, allied health, as well as numerous other disciplines, for the purposes of examining the grand challenge problems of the next decades. This will be a definitive meeting in that it will be the first World Congress of its type and will be held as a follow-up to the very well received Workshop On High Performance Computing In The Life Sciences and Medicine held by the University of Texas System Center For High Performance Computing in 1990. Young scientists (graduate students, postdocs, etc.) are encouraged to attend and to present their work in this increasingly interesting discipline. Funding is being solicited from NSF, NIH, DOE, Darpa, EPA, and private foundations, as well as other sources to assist in travel support and in the offsetting of expenses for those unable to attend otherwise. Papers, poster presentations, tutorials, focused topic workshops, birds of a feather groups, demonstrations, and other suggestions are also solicited. 2.0 CONFERENCE SCOPE AND TOPIC AREAS: The Congress has a broad scope. If you are not sure whether or not your subject fits the Congress scope, contact the conference organizers at one of the addresses below. Subject areas include but are not limited to: *Visualization/Sonification --- medical imaging --- molecular visualization as a clinical research tool --- simulation visualization --- microscopy --- visualization as applied to problems arising in computational molecular biology and genetics or other non-traditional disciplines --- telemedicine *Computational Molecular Biology and Genetics --- computational ramifications of clinical needs in the Human Genome, Plant Genome, and Animal Genome Projects --- computational and grand challenge problems in molecular biology and genetics --- algorithms and methodologies --- issues of multiple datatype databases *Computational Pharmacology, Pharmacodynamics, Drug Design *Computational Chemistry as Applied to Clinical Issues *Computational Cell Biology, Physiology, and Metabolism --- Single cell metabolic models (red blood cell) --- Cancer models --- Transport models --- Single cell interaction with external factors models (laser, ultrasound, electrical stimulus) *Computational Physiology and Metabolism --- Renal System --- Cardiovascular dynamics --- Liver function --- Pulmonary dynamics --- Auditory function, coclear dynamics, hearing --- Reproductive modeling: ovarian dynamics, reproductive ecotoxicology, modeling the hormonal cycle --- Metabolic Databases and metabolic models *Computational Demography, Epidemiology, and Statistics/Biostatistics --- Classical demographic, epidemiologic, and biostatistical modeling --- Modeling of the role of culture, poverty, and other sociological issues as they impact healthcare --- Morphometrics *Computational Disease Modeling --- AIDS --- TB --- Influenza --- Statistical Population Genetics Of Disease Processes --- Other *Computational Biofluids --- Blood flow --- Sperm dynamics --- Modeling of arteriosclerosis and related processes *Computational Dentistry, Orthodontics, and Prosthetics *Computational Veterinary Medicine --- Computational issues in modeling non-human dynamics such as equine, feline, canine dynamics (physiological/biomechanical) *Computational Allied Health Sciences --- Physical Therapy --- Neuromusic Therapy --- Respiratory Therapy *Computational Radiology --- Dose modeling --- Treatment planning *Computational Surgery --- Simulation of surgical procedures in VR worlds --- Surgical simulation as a precursor to surgical intervention --- The Visible Human *Computational Cardiology *Computational Nursing *Computational Models In Chiropractice *Computational Neurobiology and Neurophysiology --- Brain modeling --- Single neuron models --- Neural nets and clinical applications --- Neurophysiological dynamics --- Neurotransmitter modeling --- Neurological disorder modeling (Alzheimer's Disease, for example) --- The Human Brain Project *Computational Models of Psychiatric and Psychological Processes *Computational Biomechanics --- Bone Modeling --- Joint Modeling *Computational Models of Non-traditional Medicine --- Acupuncture --- Other *Computational Issues In Medical Instrumentation Design and Simulation --- Scanner Design --- Optical Instrumentation *Ethical issues arising in the use of computational technology in medical diagnosis and simulation *The role of alternate reality methodologies and high performance environments in the medical and public health disciplines *Issues in the use of high performance computing environments in the teaching of health science curricula *The role of high performance environments for the handling of large medical datasets (high performance storage environments, high performance networking, high performance medical records manipulation and management, metadata structures and definitions) *Federal and private support for transdisciplinary research in computational medicine and public health 3.0 CONFERENCE COMMITTEE *CONFERENCE CHAIR: Matthew Witten, UT System Center For High Performance Computing, Austin, Texas m.witten@chpc.utexas.edu *CURRENT CONFERENCE DIRECTORATE: Regina Monaco, Mt. Sinai Medical Center Dan Davison, University of Houston Chris Johnson, University of Utah Lisa Fauci, Tulane University Daniel Zelterman, University of Minnesota Minneapolis James Hyman, Los Alamos National Laboratory Richard Hart, Tulane University Dennis Duke, SCRI-Florida State University Sharon Meintz, University of Nevada Los Vegas Dean Sittig, Vanderbilt University Dick Tsur, UT System CHPC Dan Deerfield, Pittsburgh Supercomputing Center Istvan Gyori, University of Veszprem (Hungary) Don Fussell, University of Texas at Austin Ken Goodman, University Of Miami School of Medicine Martin Hugh-Jones, Louisiana State University Stuart Zimmerman, MD Anderson Cancer Research Center John Wooley, DOE Sylvia Spengler, University of California Berkeley Robert Blystone, Trinity University Gregory Kramer, Santa Fe Institute Franco Celada, NYU Medical Center David Robinson, NIH, NHLBI Jane Preson, MCC Peter Petropoulos, Brooks Air Force Base Marcus Pandy, University of Texas at Austin George Bekey, University of Southern California Stephen Koslow, NIH, NIMH Fred Bookstein, University of Michigan Ann Arbor Dan Levine, University of Texas at Arlington Richard Gordon, University of Manitoba (Canada) Stan Zeitz, Drexel University Marcia McClure, University of Nevada Las Vegas Renato Sabbatini, UNICAMP/Brazil (Brazil) Hiroshi Tanaka, Tokyo Medical and Dental University (Japan) Shusaku Tsumoto, Tokyo Medical and Dental University (Japan) Additional conference directorate members are being added and will be updated on the anonymous ftp list as they agree. 4.0 CONTACTING THE CONFERENCE COMMITTEE: To contact the congress organizers for any reason use any of the following pathways: ELECTRONIC MAIL - compmed94@chpc.utexas.edu FAX (USA) - (512) 471-2445 PHONE (USA) - (512) 471-2472 GOPHER: log into the University of Texas System-CHPC select the Computational Medicine and Allied Health menu choice ANONYMOUS FTP: ftp.chpc.utexas.edu cd /pub/compmed94 POSTAL: Compmed 1994 University of Texas System CHPC Balcones Research Center 10100 Burnet Road, 1.154CMS Austin, Texas 78758-4497 5.0 SUBMISSION PROCEDURES: Authors must submit 5 copies of a single-page 50-100 word abstract clearly discussing the topic of their presentation. In addition, authors must clearly state their choice of poster, contributed paper, tutorial, exhibit, focused workshop or birds of a feather group along with a discussion of their presentation. Abstracts will be published as part of the preliminary conference material. To notify the congress organizing committee that you would like to participate and to be put on the congress mailing list, please fill out and return the form that follows this announcement. You may use any of the contact methods above. If you wish to organize a contributed paper session, tutorial session, focused workshop, or birds of a feather group, please contact the conference director at mwitten@chpc.utexas.edu . The abstract may be submitted electronically to compmed94@chpc.utexas.edu or by mail or fax. There is no official format. 6.0 CONFERENCE DEADLINES AND FEES: The following deadlines should be noted: 1 November 1993 - Notification of intent to organize a special session 15 December 1993 - Abstracts for talks/posters/ workshops/birds of a feather sessions/demonstrations 15 January 1994 - Notification of acceptance of abstract 15 February 1994 - Application for financial aid 1 April 1994 - Registration deadline (includes payment of all fees) Fees include lunches for three days, all conference registration materials, the reception, and the sit down banquet: $400.00 Corporate $250.00 Academic $150.00 Student Students are required to submit verification of student status. The verification of academic status form appears appended to the registration form in this announcement. Because financial aid may be available for minority students, faculty, and for individuals from declared minority institutions, you may indicate that you are requesting financial aid as a minority individual. Additionally, we anticipate some support for women to attend. Application for financial aid is also appended to the attached form. 7.0 CONFERENCE PRELIMINARY DETAILS AND ENVIRONMENT LOCATION: Hyatt Regency Hotel, Austin, Texas, USA DATES: 24-28 April 1994 The 1st World Congress On Computational Medicine, Public Health, and Biotechnology will be held at the Hyatt Regency Hotel, Austin, Texas located in downtown Austin on the shores of Town Lake, also known as the Colorado River. The Hyatt Regency has rooms available for the conference participants at a special rate of $79.00/night for single or double occupancy, with a hotel tax of 13%. The Hyatt accepts American Express, Diner's Club, Visa, MasterCard, Carte Blanche, and Discover credit cards. This room rate will be in effect until 9 April 1994 or until the block of rooms is full. We recommend that you make your reservations as soon as possible. You may make your reservations by calling (512) 477-1234 or by returning the enclosed reservation form. Be certain to mention that you are attending the First World Congress On Computational Medicine, Public Health, and Biotechnology if you make your reservations by telephone. The hotel is approximately, five miles (15 minutes from Robert Mueller Airport). The Hyatt offers courtesy limousine service to and from the airport between the hours of 6:00am and 11:00pm. You may call them from the airport when you arrive. If you choose to use a taxi, expect to pay approximately $8.00. Automobiles may be rented, at the airport, from most of the major car rental agencies. However, because of the downtown location of the Congress and access to taxis and to bus service, we do not recommend that you rent an auto unless you are planning to drive outside of the city. Should you not be able to find an available room at the Hyatt Regency, we have scheduled an "overflow" hotel, the Embassy Suites, which is located directly across the street from the Hyatt Regency. If, due to travel expense restrictions, you are unable to stay at either of these two hotels, please contact the conference board directly and we will be more than happy to find a hotel near the conference site that should accommodate your needs. Austin, the state capital, is renowned for its natural hill-country beauty and an active cultural scene. Several hiking and jogging trails are within walking distance of the hotel, as well as opportunities for a variety of aquatic sports. From the Hyatt, you can "Catch a Dillo" downtown, taking a ride on our delightful inner-city, rubber-wheeled trolley system. In Austin's historic downtown area, you can take a free guided tour through the State Capitol Building, constructed in 1888. Or, you can visit the Governor's Mansion, recognized as one of the finest examples of 19th Century Greek Revival architecture and housing every Texas governor since 1856. Downtown you will find the Old Bakery and Emporium, built by Swedish immigrant Charles Lundberg in 1876 and the Sixth Street/Old Pecan Street Historical District - a seven-block renovation of Victorian and native stone buildings, now a National Registered Historic District containing more than 60 restaurants, clubs, and shops to enjoy. The Laguna Gloria Art Museum, the Archer M. Huntington Art Gallery, the LBJ Library and Museum, the Neill-Cochran Museum House, and the Texas Memorial Museum are among Austin's finest museums. The Umlauf Sculpture Garden, has become a major artistic attraction. Charles Umlauf's sculptured works are placed in a variety of elegant settings under a canopy of trees. The Zilker Gardens contains many botanical highlights such as the Rose Garden, Oriental Garden, Garden of the Blind, Water Garden and more. Unique to Austin is a large population of Mexican free-tailed bats which resides beneath the Congress Avenue Bridge. During the month of April, the Highland Lakes Bluebonnet Trail celebrates spring's wildflowers (a major attraction) as this self-guided tour winds through the surrounding region of Austin and nearby towns (you will need to rent a car for this one). Austin offers a number of indoor shopping malls in every part of the city; The Arboretum, Barton Creek Square, Dobie Mall, and Highland Mall, to name a few. Capital Metro, Austin's mass transit system, offers low cost transportation throughout Austin. Specialty shops, offering a wide variety of handmade crafts and merchandise crafted by native Texans, are scattered throughout the city and surrounding areas. Dining out in Austin, you will have choices of American, Chinese, Authentic Mexican, Tex-Mex, Italian, Japanese, or nearly any other type of cuisine you might wish to experience, with price ranges that will suit anyone's budget. Live bands perform in various nightclubs around the city and at night spots along Sixth Street, offering a range of jazz, blues, country/Western, reggae, swing, and rock music. Day temperatures will be in the 80-90(degrees F) range and fairly humid. Evening temperatures have been known to drop down into the 50's (degrees F). Cold weather is not expected so be sure to bring lightweight clothing with you. Congress exhibitor and vendor presentations are also being planned. 8.0 CONFERENCE ENDORSEMENTS AND SPONSORSHIPS: Numerous potential academic sponsors have been contacted. Currently negotiations are underway for sponsorship with SIAM, AMS, MAA, IEEE, FASEB, and IMACS. Additionally AMA and ANA continuing medical education support is being sought. Information will be updated regularly on the anonymous ftp site for the conference (see above). Currently, funding has been generously supplied by the following agencies: University of Texas System - CHPC U.S. Department of Energy ================== REGISTRATION FORM =============== (Please list your name below as it will appear on badge.) First Name : Middle Initial (if available): Family Name: Your Professional Title: [ ]Dr. [ ]Professor [ ]Mr. [ ]Mrs. [ ]Ms. [ ]Other:__________________ Office Phone (desk): Home/Evening Phone (for emergency contact): Fax: Electronic Mail (Bitnet): Electronic Mail (Internet): Postal Address: Institution or Center: Building Code: Mail Stop: Street Address1: Street Address2: City: State: Zip or Country Code: Country: Please list your three major interest areas: Interest1: Interest2: Interest3: Registration fee: $____________ Late fee $50 (if after April 1, 1994) $____________ **IF UT AUSTIN, PLEASE PROVIDE YOUR: UNIVERSITY ACCT. #: ______________________ UNIVERSITY ACCT. TITLE: ______________________ NAME OF ACCT. SIGNER: ______________________ ===================================================== VERIFICATION OF STUDENT STATUS Name: Mailing Address: University at which you are a student: What level student(year): Your student id number: Name of your graduate or postdoctoral advisor: Telephone number for your advisor: By filling in this section, I agree that I am electronically signing my signature to the statement that I am currently a student at the above university. ======================================================= REQUEST FOR FINANCIAL AID Name: Mailing Address: I request financial assistance under one or more of the following categories: [ ] Student (You must fill out the Verification of Student Status Section in order to be considered for financial aid under this category) [ ] Academic [ ] Minority [ ] Female [ ] Black [ ] Hispanic [ ] Native American Indian [ ] Other This form is not meant to invade your personal privacy in any fashion. However, some of the grant funds are targeted at specific ethnic/minority groups and need to be expended appropriately. None of these forms will be in any way released to the public. And, after the congress, all of the financial aid forms will be destroyed. No records will be kept of ethnic or racial backgrounds. If you have any questions concerning financial aid support, please contact Matthew Witten at the above addresses. ============================================================== From owner-embldatabank@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!olivea!spool.mu.edu!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!wfischer From: wfischer@bio.indiana.edu (Will Fischer) Newsgroups: bionet.molbio.embldatabank Subject: Software to Parse Feature Table Summary: how to automatically extract featured sequence? Message-ID: Date: 15 Sep 93 21:15:09 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 16 Nntp-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [version 1.1 PL8] I need to extract given pieces of sequence from a set of EMBL/GenBank flat file entries (as retrieved from NCBI's email server), using ranges defined in the features table. For example, I'd like to be able to extract, from a set of entries, the DNA sequence for each exon, or again for every complete CDS feature (all exons assembled). Surely not everyone does this manually? What software exists that can actually parse the (eminently parsible) joint features table format? Please post reviews of programs you have used, or mail me directly and I will summarize. Thanks, -- Will Fischer From owner-embldatabank@net.bio.net Wed Sep 15 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uunet!olivea!pagesat!decwrl!tribune.usask.ca!mizar.cc.umanitoba.ca!frist From: frist@ccu.umanitoba.ca Newsgroups: bionet.molbio.embldatabank Subject: Re: Software to Parse Feature Table Message-ID: Date: 16 Sep 93 20:55:08 GMT References: Sender: news@ccu.umanitoba.ca Organization: University of Manitoba, Winnipeg, Manitoba, Canada Lines: 62 Nntp-Posting-Host: norton.cc.umanitoba.ca In article wfischer@bio.indiana.edu (Will Fischer) writes: > >I need to extract given pieces of sequence from a set of EMBL/GenBank >flat file entries (as retrieved from NCBI's email server), using ranges >defined in the features table. For example, I'd like to be able to >extract, from a set of entries, the DNA sequence for each exon, or >again for every complete CDS feature (all exons assembled). > >Surely not everyone does this manually? > >What software exists that can actually parse the (eminently parsible) >joint features table format? Please post reviews of programs you have >used, or mail me directly and I will summarize. > >Thanks, > >-- Will Fischer > If you're working in a Unix environment, the XYLEM package can do what you want. At present, only Pascal source and SUN Sparc executable code are available. I now have a version in C that is in the testing stage and should be released in the next few weeks. While the technical problem of parsing features is difficult, XYLEM demonstrates that it can be done. The much more formidable problem comes from errors and inconsistencies in the database itself. Many words on this subject have been written by me and others in bionet.* over the last few years. Recognizing that we're going to have to live with these problems for years to come, XYLEM has capabilities that facilitate human intervention where necessary. =========================================================== X Y L E M =========================================================== XYLEM is a package of tools designed to exploit the Unix environment to enable the user to identify, extract and manipulate data from major databases such as GenBank, EMBL and PIR. Fundamental to the power of these programs is the ability to perform operations on groups of sequences, represented by names or accession numbers which function as virtual database subsets. The most powerful program is FEATURES, which uses the GETOB parser to evaluate GenBank/EMBL/DDBJ Features Table expressions, thereby extract features (eg. mRNA, sig_peptide, intron) from lists of entries. Additional programs perform operations such as translation or randomization of datasets, and formatting of multiply-aligned sequences for publication. XYLEM is compatible with the Fristensky Sequence Analysis Package, and the Pearson FASTA programs, and can be used from within the Genetic Data Environment (GDE) of Steven Smith. FTP: psgendb/xylem.tar.Z at ftp.cc.umanitoba.ca (130.179.16.8) =============================================================================== Brian Fristensky | Department of Plant Science | A question is like a knife that slices University of Manitoba | through the stage backdrop and gives us Winnipeg, MB R3T 2N2 CANADA | a look at what lies hidden behind. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Milan Kundera, THE UNBEARABLE LIGHTNESS FAX: 204-261-5732 | OF BEING =============================================================================== From owner-embldatabank@net.bio.net Tue Sep 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!mcsun!sun4nl!news.sara.nl!HASARA11.SARA.NL!A428ENDE From: A428ENDE@HASARA11.SARA.NL Newsgroups: bionet.molbio.embldatabank Subject: Re: Software to Parse Feature Table Message-ID: <16C50DE8D.A428ENDE@HASARA11.SARA.NL> Date: 22 Sep 93 09:23:48 GMT References: Organization: S.A.R.A. Academic Computing Services Amsterdam Lines: 28 Nntp-Posting-Host: vm1.sara.nl X-Newsreader: NNR/VM S_1.3.2 In article wfischer@bio.indiana.edu (Will Fischer) writes: >I need to extract given pieces of sequence from a set of EMBL/GenBank >flat file entries (as retrieved from NCBI's email server), using ranges >defined in the features table. For example, I'd like to be able to >extract, from a set of entries, the DNA sequence for each exon, or >again for every complete CDS feature (all exons assembled). > >Surely not everyone does this manually? > >What software exists that can actually parse the (eminently parsible) >joint features table format? Please post reviews of programs you have >used, or mail me directly and I will summarize. > A few months ago I wanted all the CDS from Chlamydomonas sequences. Because I d idn'T konow of any software I wrote a TurboPascal routine to do it. However the re are a lot of strange ways in the feature table to give the CDS (I found at l east five different ways!). Therefor the program isn't straight forward and is sometimes not very elegant. I think you can understand how it is working, so I can mail it if you want. It is a unit for TurboPascal 5.0 or greater and works on a DOS machine. However don't expect to much because human intervention is still necessary for some sequences because they have contradictionary feature tables. I first scree ned for this sequences and then the correct ones were copied and analyzed by th e same program. Email me if you want the source code. Henk van de Kamer CHLAMY@SARA.NL From owner-embldatabank@net.bio.net Tue Sep 21 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.embldatabank Subject: Re: Software to Parse Feature Table Message-ID: <1993Sep22.045344.7218@comp.bioz.unibas.ch> Date: 22 Sep 93 04:53:44 GMT References: <16C50DE8D.A428ENDE@HASARA11.SARA.NL> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 35 Nntp-Posting-Host: biox.embnet.unibas.ch In article <16C50DE8D.A428ENDE@HASARA11.SARA.NL>, A428ENDE@HASARA11.SARA.NL writes: |> In article |> wfischer@bio.indiana.edu (Will Fischer) writes: |> |> >I need to extract given pieces of sequence from a set of EMBL/GenBank |> >flat file entries (as retrieved from NCBI's email server), using ranges |> >defined in the features table. For example, I'd like to be able to |> >extract, from a set of entries, the DNA sequence for each exon, or |> >again for every complete CDS feature (all exons assembled). |> > > A few months ago I wanted all the CDS from Chlamydomonas sequences. Because I d |> idn'T konow of any software I wrote a TurboPascal routine to do it. However the |> re are a lot of strange ways in the feature table to give the CDS (I found at l |> east five different ways!). Therefor the program isn't straight forward and is |> sometimes not very elegant. I think you can understand how it is working, so I |> can mail it if you want. It is a unit for TurboPascal 5.0 or greater and works |> on a DOS machine. The SRS program from Thure Etzold runs on VMS and a zoo of UNIXes ; it does what you want after GCG reformatting. Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-embldatabank@net.bio.net Thu Sep 30 23:00:00 1993 Path: biosci!GENETICS.COM!mcolbert From: mcolbert@GENETICS.COM Newsgroups: bionet.molbio.embldatabank Subject: Information on wire transfer of money to EMBL Message-ID: <9310011220.AA00669@genetics.com> Date: 1 Oct 93 12:20:09 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 20 Hello, I hope someone can help me. We are trying to subscribe to the EMBL Data Library Subscription. We placed our order and received a letter stating that we had to do a wire transfer of the money for the subscription. This is fine, but our finance department needs certain information in order to perform this transaction. We faxed EMBL on 9/10/93 and haven't heard back yet. The information we need is as follows: Receiving Bank Name (the name of EMBL's bank) Receiving Bank Address Bank Sort Code (Foreign) Beneficiary Account Name Beneficiary Account # Please respond to me directly at mcolbert@genetics.com since I do not subscribe to this conference. Thanks in advance for your help. -Maureen Colbert