From owner-gdb@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!news.moneng.mei.com!howland.reston.ans.net!newsserver.jvnc.net!newsserver.cshl.org!newsserver.cshl.org!not-for-mail From: reed@phage.cshl.org (Corp Reed in CompBio) Newsgroups: bionet.molbio.gdb,bionet.software,comp.sys.mac.scitech Subject: GDB/Accessor Message-ID: <2dvn3hINN38i@phage.cshl.org> Date: 6 Dec 93 16:37:05 GMT Organization: Cold Spring Harbor Lab, NY Lines: 26 Xref: biosci bionet.molbio.gdb:140 bionet.software:6662 comp.sys.mac.scitech:719 NNTP-Posting-Host: phage.cshl.org Hi. We're going to release a new version of GDB/Accessor soon, and we'd like to ask the users of GDB/Accessor some questions. GDB/Accessor knows when it needs to be updated. The first time that you start the program after the update becomes available, it will tell you about the update and provide some short instructions on how to do it. First, if you'd like to make any bug reports or suggestions, we'd like to see them. Generally, the best place to send questions and suggestions is help@gdb.org. I'm posting this article to relevant groups to find out if people have any suggestions for additions to the manual. When the program was being beta-tested, people had trouble figuring out the map strings and asked if we could include information on how to use them. I added the "Interpreting map strings" section of the manual (which I got from GDB's anonymous FTP site) as a result. Please send any requests to reed@cshl.org. Thanks, Corprew Reed reed@cshl.org From owner-gdb@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!newsserver.jvnc.net!newsserver.cshl.org!newsserver.cshl.org!not-for-mail From: reed@phage.cshl.org (Corp Reed in CompBio) Newsgroups: bionet.molbio.gdb,bionet.software,comp.sys.mac.scitech Subject: GDB/Accessor Message-ID: <2dvn3hINN38i@phage.cshl.org> Date: 6 Dec 93 16:37:05 GMT Organization: Cold Spring Harbor Lab, NY Lines: 26 Xref: biosci bionet.molbio.gdb:141 bionet.software:6663 comp.sys.mac.scitech:720 NNTP-Posting-Host: phage.cshl.org Hi. We're going to release a new version of GDB/Accessor soon, and we'd like to ask the users of GDB/Accessor some questions. GDB/Accessor knows when it needs to be updated. The first time that you start the program after the update becomes available, it will tell you about the update and provide some short instructions on how to do it. First, if you'd like to make any bug reports or suggestions, we'd like to see them. Generally, the best place to send questions and suggestions is help@gdb.org. I'm posting this article to relevant groups to find out if people have any suggestions for additions to the manual. When the program was being beta-tested, people had trouble figuring out the map strings and asked if we could include information on how to use them. I added the "Interpreting map strings" section of the manual (which I got from GDB's anonymous FTP site) as a result. Please send any requests to reed@cshl.org. Thanks, Corprew Reed reed@cshl.org From owner-gdb@net.bio.net Mon Dec 06 22:00:00 1993 Path: biosci!JUDY.ENG.UCI.EDU!liang From: liang@JUDY.ENG.UCI.EDU (liang) Newsgroups: bionet.molbio.gdb Subject: CHINESES_BIOTECH_NET_FOUNDED Message-ID: <9312061945.AA20492@judy.eng.uci.edu> Date: 6 Dec 93 19:45:49 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 CBNet (Chinese Biotechnology Network) is a non-profit organization composed of professionals in biological, chemical, medical sciences, engineering and related fields. The CBNet sponsors the Chinese Biotechnology Internet Forum (CBIF) newsletter. To subscribe CBIF, please send an email to Listserv@UCSD.Edu with the message body: Add CB-Net. From owner-gdb@net.bio.net Mon Dec 06 22:00:00 1993 Path: biosci!JUDY.ENG.UCI.EDU!liang From: liang@JUDY.ENG.UCI.EDU (liang) Newsgroups: bionet.molbio.gdb Subject: CHINESES_BIOTECH_NET_FOUNDED Message-ID: <9312060500.AA19389@judy.eng.uci.edu> Date: 6 Dec 93 05:00:56 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 CBNet (Chinese Biotechnology Network) is a non-profit organization composed of professionals in biological, chemical, medical sciences, engineering and related fields. The CBNet sponsors the Chinese Biotechnology Internet Forum (CBIF) newsletter. To subscribe CBIF, please send an email to Listserv@UCSD.Edu with the message body: Add CB-Net. From owner-gdb@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!news From: help@gdb.org (GDB User Support) Newsgroups: bionet.molbio.gdb Subject: New GDB User Guide for 5.2 available on FTP Message-ID: <1993Dec7.203357.8328@news.gdb.org> Date: 7 Dec 93 20:33:57 GMT Sender: news@news.gdb.org Reply-To: help@gdb.org Organization: The Johns Hopkins University - Genome Data Base (GDB) Lines: 11 Nntp-Posting-Host: sif.gdb.org The GDB User Guide has been revised for version 5.2 and is now available in compressed PostScript format on the gdb ftp server (ftp.gdb.org) in the directory gdb-5.2/doc gdb52_pg1-37.ps.Z (Part 1) gdb52_pg38-72.ps.Z (Part 2) This new documentation includes examples of using the new Output Manager. If you have any problems downloading or printing these files, please send email to help@gdb.org From owner-gdb@net.bio.net Thu Dec 09 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!sol.ctr.columbia.edu!caen!batcomputer!ghost.dsi.unimi.it!genes!valeria From: valeria@genes.icgeb.trieste.it (Valeria Bevilacqua) Newsgroups: bionet.molbio.hiv,bionet.molbio.gdb,bionet.plants Subject: Mail server for protein domain funct. homologies - ICGEB Trieste Message-ID: <1993Dec10.085535.13725@genes.icgeb.trieste.it> Date: 10 Dec 93 08:55:35 GMT Organization: ICGEB Lines: 147 Xref: biosci bionet.molbio.hiv:273 bionet.molbio.gdb:145 bionet.plants:2247 SS BBB A SS EEEE H H EEEE L PPP S S B B A A S S E H H E L P P S B B A A S E H H E L P P S BB AAAAA S EEE HHHHH EEE L PPP S B B A A S E H H E L P S B B A A S E H H E L P S S B B A A S S E H H E L P SSS BBB A A SSS EEEE H H EEEE LLLL P ---------------------------------- This is the help file of the SBASE Email Server at the International Centre for Genetic Engineering and Biotechnology AREA Science Park, Padriciano 99, 34012 Trieste, Italy. ---------------------------------- The SBASE Email Server is at present experimental. Please send comments to sbase-comment@icgeb.trieste.it. Thanks. The SBASE e-mail server accepts a specially formatted mail message containing a protein query sequence, and, as a response, it sends the list of the most probable domain homologies. A database search is performed against the SBASE library of protein domains using the BLAST algorithm, and the search results, provided with annotations, are returned in a mail message. How to use: Getting HELP: ============ This help file can be gotten by sending an email to sbase@icgeb.trieste.it containing the word HELP alone in the first line of the message body. Making a QUERY: =============== Send e-mail to sbase@icgeb.trieste.it using the below example Note: the parameters before the token BEGIN are optional, (here the defaults are listed), the lines after BEGIN are required. Example: MATRIX PAM120 SCORE PARAMETER 35 ANNOTATIONS YES BEGIN > mysequence LRNGVDINTCNQNGLNGLHLASKEGHVKMVVELLHKEIILETTTKKGNTALHIAALAGQDEVVRELVNYG GLNGLHLASKEGHVKMVVELLHKEIILETTTKKGNTALHIAALAGQDEVVRELVNYG Response time ============= Requests are handled immediately, in serial order. At present, response time is quite short and is restricted by the network load rather than CPU availability. Please note that large output files, such as sometimes occur with very short query sequences, may need a long time to traverse the net. Evaluation of the output: ========================= The output of the server are BLAST search results against the SBASE protein domain library. The output file contains the BLAST search results, organized as follows: 1) List of the best scoring domain entries. As SBASE entries are named by domain names (function, structure, etc.), this list already may give some information on the expected domain composition. 2) List of alignments. For each SBASE entry you will find the complete annotation of the domain, followed by one (or several) alignments with (different parts of) the query. If one domain is found several times in your query, you may find several alignments with the same or related entries at different parts of the query. Please note that it depends on the score parameter whether or not you see all the alignments. Do not use very low cutoff values because that results in prohibitively long output files. (For the time being, we have set the default cutoff to 35 and the minimum cutoff to 30). 3) Run statistics. This is usually not essential for the evaluation of the results; you can get a complete description of these and other blast parameters by sending a HELP message to blast.ncbi.nlm.nih.gov Important: Failure to see a homology with a known domain may be due to several reasons: i) The domain type is not (yet) included in the SBASE domain library; ii) The threshold score parameter was set too high for the domain to be detected; iii) A different scoring matrix may be necessary in order to detect the alignment with the domain type in question. In the present experimental version of the SBASE server we support only the matrices used by BLAST; "customized matrices" will be added later to the final version. Papers to reference in reporting results: ========================================= Pongor, S., Skerl, V., Cserzo, M. and Hatsagi, Z., Simon, G. and Bevilacqua, V. (1992): The SBASE domain library release 2.0& A collection of annotated protein sequence segments, Nucleic Acids. Res , 21, 311-315 Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990) Basic local alignment search tool J. Mol. Biol. 215:403-410. Software availability ===================== The Sbase database is available by anonymous ftp at ftp.icgeb.trieste.it:/pub/sbase2 The blast software is available by anonymous ftp at ncbi.nlm.nih.gov:/pub/ Protection of your sequence data ================================ The query sequences are not stored in any form. Further info: ============= Server functions: Zsolt Hatsagi Tel: +39-40-3757342 Valeria Bevilacqua, systems manager (valeria@icgeb.trieste.it) Tel.: +39-40-3757330 General info: Sandor Pongor Tel: +39-40-3757300 FAX: +39-40-226-555 Mail: International Centre for Genetic Engineering and Biotechnology AREA Science Park, Padriciano 99 34012 Trieste, Italy From owner-gdb@net.bio.net Mon Dec 13 22:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.gdb Subject: IMPORTANT BIOSCI INFORMATION Date: 14 Dec 1993 02:00:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 244 Sender: kristoff@net.bio.net Distribution: bionet Message-ID: <9312141000.AA25580@net.bio.net> NNTP-Posting-Host: net.bio.net Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-gdb@net.bio.net Tue Dec 21 22:00:00 1993 Newsgroups: bionet.molbio.gdb Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!uunet!newsgate.watson.ibm.com!watnews.watson.ibm.com!hawnews.watson.ibm.com!puffin!dflash From: dflash@watson.ibm.com (The dFLASH Project) Subject: a dFLASH server update Sender: news@hawnews.watson.ibm.com (NNTP News Poster) Message-ID: Date: Wed, 22 Dec 1993 21:10:35 GMT Disclaimer: This posting represents the poster's views, not necessarily those of IBM. Nntp-Posting-Host: puffin.watson.ibm.com Organization: IBM T.J. Watson Research Lines: 371 The dFLASH group announces the availability of a new release of the dFLASH email server. The current version of the server represents a new release and features: o greatly improved sensitivity o improved mail interface o improved syntax-error checking o ability to recover text data pertaining to the retrieved sequences (see the option VERBOSE below) o new, more comprehensive protein database (we now use PIR Rel. 38) o a new computational platform o much improved alignment results o new request handling approach: all of the submitted requests will eventually be processed, independent of whether the server is running upon reception of the request; users will not receive the "server UNavailable" messages anymore, and there will be no need for re-submission. Also, *no* registration is required anymore in order to use the dFLASH server. All submitted requests will be honored, assuming that the senders' email address conforms to the accepted formats (see below). At the end, the server's help file is included with details on the use of the system. Finally, we would like to mention that we are looking forward to receiving your feedback on the current version of the server. We will greatly appreciate receiving your suggestions for modifications, comments, criticism etc which should be forwarded to dflash@watson.ibm.com (Subject: Comments). Sincerely, The dFLASH Group ---------------------------------- Cut Here ---------------------------------- !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! N O T A B E N E !! !! The dFLASH server is still under development. If some of the answers do !! !! not make sense it is very likely that this is due to a bug in our code. !! !! !! !! Reporting of such bugs will help us to incorporate all the needed fixes. !! !! !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! !! !! The database that we use is PIR Release 38 with *no* incremental updates. !! !! For more information, contact: !! !! !! !! Protein Information Resource (PIR) !! !! National Biomedical Research Foundation !! !! 3900 Reservoir Road, N.W., !! !! Washington, DC 20007, USA !! !! !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Dear User, welcome to the dFLASH server! The dFLASH server is a "homologous sequence retrieval" program for protein sequences (see also NOTES below). dFLASH is a distributed system which runs on a 16-node IBM SP/1. Although, the SP/1 has a fast interconnection network for intra-node communication, dFLASH currently uses regular TCP/IP for message delivery. Furthermore, evidence integration and alignment areperformed on a single node, instead of in parallel on all 16 nodes. As is evidenced by the difference in the total CPU usage and the elapsed wall clock time, a large portion of the total time is consumed by the network communicationand the serial processing. We will soon exploit the SP/1's fast interconnection feature and also parallelize the evidence intergation/alignment code resulting in an expected 16-fold speedup. The system has been implemented using IBM's Concert/C language for distributed programming. The server is now available 24 hours a day, 7 days a week. Meanwhile, incremental changes and improvements made to the server will be reflected in the text of this help file: it is recommended that users periodically issue a `send help' request for up to date information on the server. Effective today, November 16, 1993, *no* registration is required in order to use the dFLASH server. For the moment, we can process requests originating from email addresses of the form "user@[machine.]institution.type" or "user%machine@[machine.]institution.type" We plan to further expand the accepted formats, depending on demand. You can use the dFLASH facilities by sending an email message to "dflash@watson.ibm.com" $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ VERY IMPORTANT: the "Subject" line of the message should be one of: { dflash, --------------- dFlash, dFLASH, DFLASH }. Messages whose subject line does not conform to this rule, will be left **unprocessed**. The reason for that restriction is that we want to be able to automatically distinguish between messages that are addressed to the server and those that are meant for one of the group members. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ REQUEST FORMAT: --------------- The typical message-body of an email request looks like: PAM 250 (mandatory | DIRECTIVE) VERBOSE 10 20 (optional | DIRECTIVE) SEQUENCES 100 (optional | DIRECTIVE) ALIGNMENTS 50 (optional | DIRECTIVE) THRESHOLD 30 (optional | DIRECTIVE) BEGIN (mandatory | DIRECTIVE) >A_ONE_LINE_TEST_SEQ_LABEL (mandatory -- notice the '>' ) a_sequence_of_{amino_acids,spaces,tabs} 1 (mandatory terminator) The PAM/BLOSUM, VERBOSE, SEQUENCES, ALIGNMENTS, and THRESHOLD directives can appear in any order but they *must* precede the BEGIN directive. The BEGIN line must precede the LABEL line, and the latter must precede the test sequence. The test sequence should contain at least 30 and not more than 1,000 aminoacids. BUT it *may* contain CARRIAGE RETURNS, TABS and SPACES. There is NO case sensitivity in the label and the test sequence itself. The words appearing on the lines marked DIRECTIVE above can be in lower case or upper case; in other words, you can have pam or PAM, threshold or THRESHOLD, alignments or ALIGNMENTS, etc. However, something like ThReShOlD will not work. The VERBOSE line allows the sender to also retrieve the data about authors, dates, entries, superfamilies etc. that are contained in the original PIR database. This directive can take one or two arguments; for example: verbose 15 25 means "send me the text data for the proteins occupying positions 15 through 25 in the final ranking." On the other hand, verbose 15 means "send me the text data for the proteins occupying the first 15 positions in the final ranking." If no verbose line appears, no text data will be sent. The SEQUENCES line allows one to restrict the reported sequences to the given number. This directive controls the number of entries in the ``short list'' of recovered database sequences only. If no SEQUENCES line is given, the server code will set it to an appropriate default value. The ALIGNMENTS line allows one to restrict the reported alignments to the given number. If no ALIGNMENTS line is given, the server code will set it to an appropriate default value. The ALIGNMENTS value cannot exceed 1000. Values larger than 1000 are reduced to 1000. The THRESHOLD line allows one to restrict the number of reported sequences (and thus alignments) to only those whose Score exceeds the given THRESHOLD value. If no THRESHOLD line is given the server code will set it to an appropriate default value. The THRESHOLD value cannot be less than 30. Values smaller than 30 are increased to 30. Notice: if the THRESHOLD value is too small, you are running the danger of upsetting your mailer program since chances are that you will receive a very big file as a reply from the server. The LABEL line *must* now be preceded by the character '>'. Finally, notice that you need to terminate the sequence with the terminator '1'. Two example requests follow: Example 1: pam 250 sequences 50 alignments 30 threshold 100 begin > HBA_HUMAN STANDARD; PRT; 141 AA. P01922; HEMOGLOBIN ALPHA VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP TTKTYFPHFDLSHGSAQVKGHG KKVADALTNA V A H V D D M PNALSALSDLHAHKLRVDPVNFK llshcllvtlaahlpaeftpavhasldkflasvstvltskyr 1 Note: all amino acids from "VLSP" through "ltskyr will be used in the search. Not more than the 50 top scoring sequences will be reported in the short list. Also, the alignments for the top 30 scoring sequences will be returned. No reported sequence will have score that is less than 100. Example 2: BLOSUM 62 BEGIN > Your-Favorite-Label Goes Here VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP TTKTYFPHFDLSHGSAQVKGHG KKVADALTNA V A H V D D M PNALSALSDLHAHKLRVDPVNFK llshcllvtlaahlpaeftpavhasldkflasvstvltskyr 1 Note: all amino acids from "VLSP" through "ltskyr" will be used in the search. The server code will set the various parameters to appropriate default values. SCORING MATRICES: ----------------- You can use both PAM and BLOSUM scoring matrices. These can be requested via one of { pam, PAM, blosum, BLOSUM }. The currently supported distances are for BLOSUM: 30, 35, 40, 45, 50, 55, 60, 62, 65, 70, 75, 80, 85, 90, 100 for PAM: 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, and 500. NOTE ON ALIGNMENT: ------------------ The server's alignment code now implements dynamic programming. This is not to be confused with the indexing method that is used to determine the candidates to align. The meaning of the variables in the listing that is returned by the dFLASH server ..... .... Score Matrix: PAM250 Max Reported Sequences: 1000 Max Reported Alignments: 10 Score Threshold At: 65 Id Label: Score NRes Ex% Tot% Sig Pk ---------------------------------------------------------------------------- 1. HAHU hemoglobin alpha chain - human 655 141 100% 100% 100 89 2. HACZ hemoglobin alpha chain - chimpanzee 655 141 100% 100% 100 89 3. HACZP hemoglobin alpha chain - pygmy chi 655 141 100% 100% 100 89 4. HAGO hemoglobin alpha chain - lowland go 654 141 99% 100% 99 89 5. HAMQP hemoglobin alpha chain - hanuman l 653 141 97% 100% 99 89 6. B27792 hemoglobin alpha-1 chain - orangu 649 141 97% 100% 99 89 7. A25126 hemoglobin alpha-1 chain - Sumatr 649 141 97% 100% 99 89 ... ..... .. is the following: NRes: the number of residues (amino acids) in the recovered match Score: sequence similarity score of the recovered sequence based on the selected mutation matrix Ex%: percentage of *exact* matching residues Tot%: percentage of *total* (=exact+conservative) matching residues Sig: 100 times the ratio between the actual computed score and the score obtained by matching the retrieved sub-segment with itself; the denominator is the maximum obtainable score for the sub-segment in question (all gaps removed). Peak: the maximum score value over *any* 20 residue-window of the recovered match TO OBTAIN HELP: --------------- You can obtain this message at any moment by sending a message with one of: { dflash, dFlash, dFLASH, DFLASH } in the "Subject" line and a body containing one of { help, HELP, send help, SEND HELP }. TO OBTAIN ON-LINE REPRINTS OF PAPERS ------------------------------------ You can obtain reprints (in PostScript) of relevant papers by sending a message with one of: { dflash, dFlash, dFLASH, DFLASH } in the "Subject" line and a body containing one of {flashpaper, FLASHPAPER, send flashpaper, SEND FLASHPAPER } ---> returns to the originator of the request a copy of the FLASH paper one of {dflashpaper, DFLASHPAPER, send dflashpaper, SEND DFLASHPAPER } ---> returns to the originator of the request a copy of a paper that contains a description of dFLASH (long) one of {concertpaper, CONCERTPAPER, send concertpaper, SEND CONCERTPAPER } ---> returns to the originator of the request a copy of a high-level paper describing the CONCERT/C language one of {bayespaper, BAYESPAPER, send bayespaper, SEND BAYESPAPER } --> returns to the originator of the request a copy of a paper describing a computer-vision application based on similar to dFLASH indexing principles (long) Notice there can only be *one* such request per message! OTHER NOTES: ------------- (1) for the time being we do not incorporate incremental updates of PIR. (2) the reply from the server now contains the label on its Subject line; we thought this might be useful to some users. (3) format checking and error reporting have been improved considerably. (4) at the moment we are putting together the version of the server that will allow sequence searches in GenBank. The current projection is that the GenBank search server will be available before the middle of January. (5) dFLASH searches are currently available through GRAIL of the Oak Ridge National Laboratory. Thank you for your interest in the dFLASH server. Sincerely, The dFLASH Group ############################################################################### COMMENTS?? ---------- We will appreciate receiving your feedback, suggestions, comments, or bug reports; all of these can be sent to "dflash@watson.ibm.com" Please, make sure your "Subject" line contains the word "comments". ############################################################################### REFERENCES ---------- If you make use of the dFLASH server, please reference A. Califano and I. Rigoutsos, "FLASH: A Fast Look-up Algorithm for String Homology." In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, July 1993, Bethesda, MD. If you wish to find out more about the dFLASH server, you can contact Andrea Califano (acal@watson.ibm.com) or Isidore Rigoutsos (rigoutso@watson.ibm.com) ############################################################################### For more information on the Concert/C language, please refer to J. Auerbach, D. Bacon, A. Goldberg, G. Goldszmidt, A. Gopal, M. Kennedy, A. Lowry, J. Russell, W. Silverman, R. Strom, D. Yellin, and S. Yemini, "High-level language support for programming reliable distributed systems." In Proceedings of the International Conference on Computer Languages, April 1992, Oakland, California. or contact Josh Auerbach (jsa@watson.ibm.com) ############################################################################### ---------------------------------- Cut Here ---------------------------------- From owner-gdb@net.bio.net Sun Dec 26 22:00:00 1993 Path: biosci!rutgers!gatech!howland.reston.ans.net!nctuccca.edu.tw!TWNMOE10.Edu.TW!YMMCS023 From: YMMCS023@TWNMOE10.Edu.TW Newsgroups: bionet.molbio.gdb Subject: compare DNA sequence on anonymous DNA bank host Message-ID: <16CB21D4A.YMMCS023@TWNMOE10.Edu.TW> Date: 28 Dec 93 02:04:58 GMT Organization: MOE Computer Center, Taiwan Lines: 13 NNTP-Posting-Host: twnmoe10.edu.tw X-Newsreader: NNR/VM S_1.3.2 I got some sequences from human fetal brain cDNA. Where could I compare these uences with DNA bank (requiring no specific password) on internet to see if I h ave got something new or something old. Any information will be highly appresci ated. Sincerely CHEN-JEE HORNG, M.D. DEPARTMENT OF PSYCHIATRY VETERANS GENERAL HOSPITAL-TAIPEI TAIPEI, TAIWAN, R.O.C. From owner-gdb@net.bio.net Wed Dec 29 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!howland.reston.ans.net!gatech!destroyer!news.itd.umich.edu!geneva.csmil.umich.edu!cash From: cash@geneva.csmil.umich.edu (Howard Cash) Newsgroups: bionet.molbio.gdb Subject: Re: compare DNA sequence on anonymous DNA bank host Date: 30 Dec 1993 17:38:37 GMT Organization: Cognitive Science and Machine Intelligence Lab, U. of Michigan Lines: 33 Message-ID: <2fv3mt$4tl@terminator.rs.itd.umich.edu> References: <16CB21D4A.YMMCS023@TWNMOE10.Edu.TW> NNTP-Posting-Host: geneva.csmil.umich.edu Keywords: n > [. . .] Where could I compare these sequences > with DNA bank (requiring no specific password) on internet to see if I > have got something new or something old. > [. . .] >CHEN-JEE HORNG, M.D. >DEPARTMENT OF PSYCHIATRY >VETERANS GENERAL HOSPITAL-TAIPEI >TAIPEI, TAIWAN, R.O.C. > > A good resource is the 'GenQuest' or 'Q' server at Oak Ridge National Labs. This lets you do several kinds of searchers (BLAST, Parallel implemetation of Smith Waterman, etc.) searches against several databases (GenBank, PIR, Jurek Jurka's human repeat sequence database, etc). For information, send email to Q@ornl.gov The subject line is ignored. The message body should just include the word help Hope you find this useful. -Hobie - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Disclaimer demanded by the lord of bionet: I am also an employee of a COMMERCIAL biotech software developer. Opinions are, of course, my own. In particular, they do not reflect positions of Univ. of Michigan, CSMIL, or Gene Codes Corp. Postings should not be considered advertising for Gene Codes Corp or Sequencher. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -