From owner-embldatabank@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!hearst.acc.Virginia.EDU!murdoch!dayhoff.med.Virginia.EDU!wrp From: wrp@dayhoff.med.Virginia.EDU (William R. Pearson) Newsgroups: bionet.software,bionet.molbio.embldatabank,bionet.molbio.genbank Subject: Fasta updates Message-ID: Date: 25 Nov 93 19:56:47 GMT Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Lines: 9 Xref: biosci bionet.software:6625 bionet.molbio.embldatabank:263 bionet.molbio.genbank:1456 New versions of the FASTA package of programs are available from "virginia.EDU" in pub/fasta/fasta16c24b.shar(.Z) and pub/fasta/beta/fasta16c31a.shar(.Z). The programs have been belatedly modified to read the current EMBL format and the beta/fasta16c31.shar program has been more extensively tested (and corrected) to work with the NCBI BLASTP/N formats. Bill Pearson From owner-embldatabank@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.embldatabank Subject: CHINESES_BIOTECH_NET_FOUNDED Message-ID: <9312061945.AA20484@judy.eng.uci.edu> Date: 6 Dec 93 19:45:46 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-embldatabank@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.embldatabank Subject: CHINESES_BIOTECH_NET_FOUNDED Message-ID: <9312060500.AA19381@judy.eng.uci.edu> Date: 6 Dec 93 05:00:49 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-embldatabank@net.bio.net Wed Dec 08 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!caen!batcomputer!ghost.dsi.unimi.it!genes!pongor From: pongor@genes.icgeb.trieste.it (Sandor Pongor) Newsgroups: bionet.molbio.embldatabank Subject: Mail server for protein functional domain homologies - ICGEB Trieste Keywords: mail server, molecular biology, protein domains, sequences Message-ID: <1993Dec9.100711.21830@genes.icgeb.trieste.it> Date: 9 Dec 93 10:07:11 GMT Organization: ICGEB Lines: 148 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-embldatabank@net.bio.net Thu Dec 09 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: jclewley@crc.ac.uk (Dr. J.P. Clewley) Newsgroups: bionet.molbio.embldatabank Subject: Unavailability of published sequences with embl accession numbers Message-ID: <2ear7b$gpq@mserv1.dl.ac.uk> Date: 10 Dec 93 21:54:51 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 18 Original-To: embl-db@dl.ac.uk Sequences reported in: van Camp et al, System. Appl. Microbiol. 16, 361-368 (1993) with EMBL accession numbers x67758-x67775, described Tas availableU in the legend to Table 1 in that paper could not be found in the EMBL database of 5 December, 1993. When will these sequences be available? Jon Clewley Central Public Health Laboratory, Colindale, London, UK email: jclewley@crc.ac.uk From owner-embldatabank@net.bio.net Tue Dec 21 22:00:00 1993 Newsgroups: bionet.molbio.embldatabank 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 21:08:44 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 ----------------------------------