SAGITTARIUS PIR-44 (April 1995) variant *************************************** SAGITTARIUS PIR is a highly compact databank variant of original PIR database designed to assist individual researchers and software developers in utilization of sequence database information without huge storage space requests. It contains custom compressed PIR information and C-written interface which allow fast direct access to the stored information without total decompressing of corresponding files. Starting from PIR-41 version, one and the same databank files as well as interface C-file can be used on both PC-compatibles and UNIX V computers (with forthcoming Mac interface version), without any modifications. Interface supports all standard PIR Request Network queries (i.e. get databank SEQ number by entry; for the defined databank SEQ number, get specified information like: name, organism(s), keyword(s), sequence, sequence features with coordinates etc.). In difference with PIR Request Network, SAGITTARIUS PIR allows you to call PIR-contained information directly from your C program, even on the personal computer separated from any network. In addition, all numerical information like introns placement and concrete feature coordinates are aquired by calling program in the form of constants instead of text strings what simplifies (sub)sequence manipulations. For even larger storage compactness and flexibility, SAGITTARIUS PIR was realized in the form of separate file sets, where each file set contains database information of independent type (i.e. sequences, entry indexes, organisms etc.). On the particular computer, available configuration of the PIR information could be easily changed as needed by the user itself without any damage for retrievals of other types of stored information. For example, a file set which contains protein sequences itself and their PIR entry indexes (including reverse indexation arrays) takes less than 14Mb of disk space. For PC-compatibles (with fortcoming version for UNIX/Xwindow), a dialog shell is available which supports all standard PIR Request Network queries plus homology searches, alignments etc. SAGITTARIUS PIR is distributed freely (all databank file sets, interface C-file, test/example program C-file, PC-shell executable) via anonymous FTP. File sets and interface can be used/included in any commercially distributed package without any restrictions. Consultations and advanced interface variants (currently used to support fast effective database manipulations in other SAGITTARIUS family packages) are available from the developers upon request. For now, SAGITTARIUS PIR compressed databank stores in custom compressed form following original informational types (fields) of PIR database: - database entry index - accession number(s) - other (non-PIR) database crossreference(s) - protein name - organism name(s) - alternative protein name(s) - keyword(s) - superfamily name(s) - gene name(s) - map position(s) - unusual start codon(s) - intron(s) placement - literature reference(s), including for each: -journal or citation -author(s) -title -free-format comment - sequence feature(s) - free-format comment - protein sequence itself For PIR-44, all bank files takes 37+ Mb on hard disk (23+ Mb in transport ZIP-compressed form). Each original database informational field (i.e. sequences, organisms, names, keywords etc.) is stored in separate file set what allows the user to configure reduced bank variants by simply excluding unnecessary information files from unpacking. For example, deletion of literature references reduces the bank to only 27+ Mb. Core (minimal configuration supported by available PC-shell) variant of databank files includes only indexes and sequences. All more complete configurations could be produced by simply adding (depacking from distributive) of corresponding file sets. List of distributive files with decompressed files description ************************************************************** ------------------------------------------------------------------------------- ZipFile ZipSize Content Description ------------------------------------------------------\/ Core config part \/ CORE 12,542,278 Entry indexes + sequences itself ------------------------------------------------------\/ User-variable part \/ NAME 1,137,312 Sequence names ORGANISM 533,940 Organisms KEYWORD 322,655 Keywords S_FAMILY 168,410 Superfamily classifications CROSSREF 327,537 Other database crossreferences FEATURE 1,091,777 Sequence features GENE_MAP 29,621 Genetic map positions ALT_NAME 220,725 Sequence alternative names GENE 194,431 Genes CODON 10,430 Unusual start codons ACC_CODE 1,569,822 PIR accession codes COMMENT 285,206 Sequence comments INTRON 47,096 Intron(s) placement REF_JOU 991,882 References core : references itself REF_AUTH 1,779,989 Ref. extention : reference authors REF_TITL 2,108,161 Ref. extention : reference titles REF_COMM 63,120 Ref. extention : reference comments ------------------------------------------------------\/ Dialog shell for PC \/ PC_SHELL 194,641 PC-executable + two MAP-files (to \PIR) ------------------------------------------------------\/ Interface \/ INTERFAC 15,350 Interface and test program, C-files, PRJ file ------------------------------------------------------------------------------- SAGITTARIUS PIR Data Bank Shell ******************************* SAGITTARIUS PIR Automated Sequence Bank is a dialog shell for manipulation of the compressed sequence database information with orientation on MS DOS/Windows PC-compartibles, with installed hard disk optimizers (like Smartdrive, Hyperdisk, Ncache etc.). P5 or 486 are recommended, 386/286 will be significantly slower but still OK. The dialog data shell supports the following main operations: - selection of sequences to bank buffer by - dictionary-defined record for specified informational field (name, source, keyword, feature etc.) - user-defined context in specified informational field (name, source, keyword, feature etc.) - set of dictionary-defined records for different informational fields (source, keyword, superfamily etc.) - SEQ (non)perfect homology with user-defined short sequence - store and retrieve buffer content (SEQ bank numbers and indexes) between sessions - output user-specified (buffer) SEQ data to disk files - fast SEQ homology searches (for user-defined SEQ of length not more than 50-100 residues, only 1 hour with full PIR bank on 486/33) - fast subregion-sensitive pairwaise alignments (user-defined sequence with buffer SEQ's or full bank) - easy data access from user programs (C) as a support for applications development SAGITTARIUS data bank files are usually filled out by current available PIR database information by distributors only. Distributive variant includes ready-for-use informational files, interface and executables - all in compressed form. ----------------------------------------------------------------------------- SAGITTARIUS PIR is available by anonymous FTP from: FTP.SCRI.FSU.EDU, directory /pub/genetics/pir/ SAGITTARIUS PIR is also available by anonymous FTP from some of the well-known bio-servers (IUBIO etc.). ---------------------------------------------------------------------------- Installation on UNIX system *************************** All decompressed SAGITTARIUS databank files must be placed in one and the same directory which name should be correctly specified in the interface C-file (first strings). Placement of the 'X' symbol in the first position of the corresponding text string (instead of '/') will force interface to carry out formal check for databank files presence. Installation on PC ****************** If you plan to use PC-shell, all decompressed SAGITTARIUS databank files must be placed in the directory \PIR on any (but one and the same) logical drive. Otherwise all decompressed SAGITTARIUS databank files must be placed in one and the same directory which name should be correctly specified in the interface C-file (first strings). Placement of the 'X' symbol in the first position of the corresponding text string (instead of some drive letter) will force interface to carry out 1) search of corresponding directory on all available logical drives and 2) formal check for databank files presence. Bank executable BANK.EXE may be placed in any directory on any logical drive. Important: .MAP-files contained in the same PC-shell compressed file should be moved into the directory \PIR where other databank files are placed. It is highly reccomended to run BANK.EXE from directory (and/or logical drive) other than data location to avoid random bank files structure damage. Bank is oriented on file-server data accession and can find \PIR directory (and test them for correct data configuration) on any logical drive. ---------------------------------------------------------------------------- SAGITTARIUS PIR is a FREE DOMAIN software. This package (with compressed data files) can be redistributed freely without any limitations but only free of charge and for non-commercial usage. No changes in data files and/or executables are allowed. You may include compressed SAGITTARIUS datafiles in your application packages freely even in the case of any commercial usage. -------------------------------------------------------------- For helpful comments and discussions please contact Dr. Victor B. Strelets (strelets@scri.fsu.edu) Computational Genetics and Biophysics, Supercomputer Computations Research Institute, FSU B-186, Tallahassee, FL 32306-4052, USA --------------------------------------------------------------- For control purposes you may use following info about the SAGITTARIUS PIR distributive files (with information about compressed files): CORE ZIP 12,542,278 SEQ0 BAN 330,572 SEQ BAN 10,911,789 DIC BAN 330,888 DIC2 BAN 106,496 IND BAN 661,144 IND0 BAN 330,572 IND2 BAN 331,776 0IND REV 330,572 1IND REV 330,572 NAME ZIP 1,137,312 NAM BAN 1,135,808 NAM0 BAN 330,572 NAM2 BAN 210,944 0NAM REV 209,100 1NAM REV 330,564 ORGANISM ZIP 533,940 SOU BAN 116,480 SOU0 BAN 330,572 SOU1 BAN 84,824 SOU2 BAN 26,624 0SOU REV 26,020 1SOU REV 504,612 KEYWORD ZIP 322,655 KW BAN 20,816 KW0 BAN 330,388 KW1 BAN 121,476 KW2 BAN 6,144 0KW REV 5,672 1KW REV 323,992 GENE ZIP 194,431 GENE BAN 89,792 GENE0 BAN 279,284 GENE1 BAN 44,160 GENE2 BAN 36,864 0GENE REV 35,644 1GENE REV 58,816 ALT_NAME ZIP 220,725 ANAM BAN 151,432 ANAM0 BAN 330,368 ANAM1 BAN 45,028 ANAM2 BAN 38,912 0ANAM REV 36,956 1ANAM REV 58,772 S_FAMILY ZIP 168,410 SFAM BAN 61,360 SFAM0 BAN 278,972 SFAM1 BAN 29,064 SFAM2 BAN 14,336 0SFAM REV 14,020 1SFAM REV 134,296 ACC_CODE ZIP 1,569,822 AC BAN 751,104 AC0 BAN 330,572 AC1 BAN 377,236 AC2 BAN 376,832 0AC REV 375,552 1AC REV 375,552 CODON ZIP 10,430 CDN BAN 216 CDN0 BAN 271,464 CDN1 BAN 184 CDN2 BAN 2,048 0CDN REV 108 1CDN REV 4,668 FEATURE ZIP 1,091,777 FT BAN 323,616 FT0 BAN 309,148 FT1 BAN 328,440 FT2 BAN 53,248 FTN BAN 1,132,072 FTN0 BAN 309,148 FTN1 BAN 328,440 0FT REV 53,204 1FT REV 270,768 GENE_MAP ZIP 29,621 MAP BAN 35,888 MAP0 BAN 276,328 COMMENT ZIP 285,206 CC BAN 524,056 CC0 BAN 310,212 CROSSREF ZIP 327,537 CR BAN 416,416 CR0 BAN 330,572 INTRON ZIP 47,096 INTR0 BAN 278,936 INTR1 BAN 60,204 REF_JOU ZIP 991,882 REF BAN 1,215,520 REF0 BAN 330,572 REF1 BAN 456,592 REF_AUTH ZIP 1,779,989 AUT BAN 2,707,832 AUT0 BAN 330,572 AUT1 BAN 456,592 REF_TITL ZIP 2,108,161 TITLE BAN 3,419,552 TITLE0 BAN 330,564 TITLE1 BAN 425,216 REF_COMM ZIP 63,120 REFCOM BAN 66,488 REFCOM0 BAN 330,520 REFCOM1 BAN 37,784 PC_SHELL ZIP 194,641 BANK EXE 535,134 BANK1 MAP 165,600 BANK2 MAP 165,600 INTERFAC ZIP 15,350 INTERF C 26,237 BANK H 12,163 BANK0 H 50 INTERF H 6,048 BANKTEST C 9,795 BANKTEST PRJ 5,353 ----------------------------------------------------------------- Standard disclaimer: Author(s) will in no way be held liable for any loss of profit or any other commercial damage including but not limited to special, incidental, consequential or other damages from use of this package. You may use them only with the understanding that you use it at your own risk and that your use of the software and datafiles is your agreement to this disclaimer.