printsextract Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Extract data from PRINTS database for use by pscan Description printsextract preprocesses the PRINTS database for use with the program pscan. It derives matrix information from the final motif sets of the PRINTS data file (prints.dat). It creates files in the EMBOSS data subdirectory PRINTS these being a matrix file and files containing text information for each fingerprint. Running this program may be the job of your system manager. Usage Here is a sample session with printsextract % printsextract Extract data from PRINTS database for use by pscan PRINTS database file: prints.test Go to the input files for this example Go to the output files for this example Command line arguments Extract data from PRINTS database for use by pscan Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-infile] infile PRINTS database file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: (none) General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format Input files for usage example File: prints.test gc; ACHEFISH gx; PR00879 gn; COMPOUND(4) ga; 06-JUL-1998; UPDATE 06-JUN-1999 gt; Fish acetylcholinesterase signature gp; PRINTS; PR00878 CHOLNESTRASE; PR00880 ACHEINSECT gp; INTERPRO; IPR000908 gp; PDB; 2ACE gp; SCOP; 2ACE gp; CATH; 2ACE bb; gr; 1. VOET, D. AND VOET, J.G. gr; Biochemical communications: Hormones and neurotransmission. gr; BIOCHEMISTRY 34(4) 1298-1299 (1995). gr; gr; 2. COUSIN, X., HOTELIER, T., GILES, K., TOUTANT, J.P. AND CHATONNET, A. gr; aCHEdb: the database system for ESTHER, the a/b fold family of proteins and gr; the cholinesterase gene server. gr; NUCLEIC ACIDS RES. 26 226-228 (1998). gr; gr; 3. THE ESTHER DATABASE gr; http://meleze.ensam.inra.fr/cholinesterase/definitions.html gr; gr; 4. CHOLINESTERASES gr; http://bnlstb.bio.bnl.gov:8000/disk$3/giles/che.html bb; bb; gd; Acetylcholine is involved in the transfer of messages across a variety of gd; synapses in vertebrates and invertebrates. The diverse physiological effects gd; attributable to this molecule arise from the presence of specific receptors gd; in the postsynaptic cell membranes. Several classes of receptor are known, gd; most of which translate the binding of acetylcholine into the opening of gd; channels for the passage of ions, such as sodium and potassium. gd; gd; Acetylcholinesterase is an enzyme that catalyses the hydrolysis of gd; acetylcholine to choline and acetate: gd; gd; Acetylcholine + H(2)O -> Choline + Acetate gd; gd; The enzyme also acts on a variety of acetic esters and catalyses trans- gd; acetylations. It is found in, or attached to, cellular or basement membranes gd; of presynaptic cholinergic neurons and postsynaptic cholinoceptive cells. gd; To prevent continuous firing of nerve impulses, acetylcholinesterase has a gd; high K(cat) (~14000/s), to ensure that acetylcholine is broken down quickly. gd; gd; Cholinesterases constitute a family of enzymes that fall into two main gd; types, depending on their substrate preference: enzymes that preferentially gd; hydrolyse acetyl esters are termed acetylcholinesterase (AChE) (EC 3.1.1.7); gd; and those that prefer other types of ester, such as butyrylcholine are gd; termed butyrylcholinesterase (BChE) (EC 3.1.1.8). [Part of this file has been deleted for brevity] fd; YFISGFLFYLATIINPIAYNLASSRFR Q18701 323 17 fd; FIISMLLASLNSCCNPWIYMFFAGHLF Q90334 311 13 fd; YKITRPLASANSCLDPVLYFLAGQRLV P2UR_RAT 287 20 fd; AAMPAYFAKSATIYNPIIYVFMNRQFR OPSR_CARAU 301 13 fd; AQWFIVLAVLNSAMNPVIYTLASKEMR EDG3_HUMAN 280 14 fd; YKVTRPLASANSCLDPVLYFLAGQRLV P2UR_HUMAN 288 20 fd; YKITRPLASANSCLDPVLYFLAGQRLV P2UR_MOUSE 288 20 fd; AAMPAYFAKSATIYNPVIYVFMNRQFR OPSR_ORYLA 301 13 fd; MAIPSFFSKSSALFNPIIYILLNKQFR OPSG_ORYLA 289 13 fd; THFAFALQYINSAANPFLYVFLSDSFQ Q23033 401 16 fd; FTAITWISFSSSASKPTLYSIYNANFR GPRJ_HUMAN 312 13 fd; AALPAYFAKSATIYNPIIYVFMNRQFR OPSR_CAPHI 304 13 fd; YINIYWLGMSSTVFNPVIYYFMNKRFR O44148 323 16 fd; LHFTVCLMNFNCCMDPFIYFFACKGYK EBI2_HUMAN 290 23 fd; FTAVTWVSFSSSASKPTLYSIYNANFR GPRJ_MOUSE 306 13 fd; NYTGINMASLNSCIGPVALYFVSRKFK ET3R_XENLA 365 36 fd; TIWGSVFAKANSCYNPIVYGISHPRYK OPS2_LIMPO 310 13 fd; YLVALCLSTLNSCIDPFVYYFVSKDFR PAR2_MOUSE 328 16 fd; YIVALCLSTLNSCIDPFVYYFVSHDFR PAR2_HUMAN 326 16 fd; YLVALCLSTLNSCIDPFVYYFVSKDFR PAR2_RAT 326 16 fd; YILSACVGSVSCCLDPLIYYYASSQCQ THRR_XENLA 348 13 fd; TIWGSVFAKANAVYNPIVYGISHPKYR O76125 317 12 fd; TIWGSVFAKANSCYNPIVYGISHPRYK OPS1_LIMPO 310 13 fd; YLIALCLGSLNSCLDPFLYFVMSKVVD PAR3_MOUSE 339 16 fd; TIWGSVFAKANAVYNPIVYGISHPKYR O76123 317 12 fd; YLLCVCVTSVASCIDPLIYYYASSECQ THRR_RAT 360 17 fd; VHVAEIVSLCHCFINPLIYAFCSREFT VQ3L_CAPVK 337 21 fd; TIWGSLFAKANAVFNPIVYGISHPKYR OPS1_SCHGR 315 12 fd; AAAPAFFSKTAAVYNPVIYVFMNKQVS OPSO_SALSA 286 13 fd; YHFSLLLTSFNCVADPVLYCFVSETTH O46685 268 17 fd; KILLVLFYPINSCANPFLYAIFTKNFR FSHR_HORSE 607 13 fd; YIFCHLVGISSTCVNPIVYALVNESFR O44690 308 12 fd; YLLCVCVSSISSCIDPLIYYYASSECQ THRR_HUMAN 353 17 fd; AALPAYFAKSATIYNPIIYVFMNRQFR OPSR_XENLA 303 13 fd; ITFSETISLARCCINPIIYTLIGEHVR VK02_SPVKA 312 24 fd; YHSSLAFTSLNCVADPILYCLVNEGAR GPR4_HUMAN 268 21 fd; YHFSLLLTSFNCVADPVLYCFVSETTH OGR1_HUMAN 268 17 fd; YHSSLAFTSLNCVADPILYCLVNEGAR GPR4_PIG 268 21 fd; TIWGSLFAKANAVYNPIVYGISHPKYR OPSD_CAMAB 315 12 fd; TIWGSLFAKANAVYNPIVYGISHPKYR OPSD_CATBO 315 12 fd; KILLVFFYPLNSCADPYLYAILTSQYR Q94979 738 13 fd; TIWGACFAKSAACYNPIVYGISHPKYG OPS1_CALVI 309 12 fd; KILLVLFYPINSCANPFLYAIFTKTFR FSHR_CHICK 608 13 fd; KILLVLFYPINSCANPFLYAIFTKNFR FSHR_EQUAS 600 13 fd; TMLPAVFAKTVSCIDPWIYAINHPRYR OPSB_APIME 318 13 fd; TMIPAVTAKIVSCIDPWVYAINHPRFR OPS2_SCHGR 315 13 fd; TIWGACFAKSAACYNPIVYGISHPKYR OPS1_DROME 311 12 fd; TIWGSLFAKANAVYNPIVYGISHPKYR OPSD_APIME 313 12 fd; SMLPCLACKSVSCLDPWVYATSHPKYR OPS5_DROME 314 13 fd; TICGSVFAKANAVCNPIVYGLSHPKYK OPS6_DROME 309 12 bb; The input file must be the "prints.dat" file of a PRINTS distribution. The PRINTS database is currently available via the anonymous ftp servers at: * Manchester ftp://bioinf.man.ac.uk/pub/prints/ * EBI ftp://ftp.ebi.ac.uk/pub/databases/ * EMBL ftp://ftp.embl-heidelberg.de/ * NCBI ftp://ncbi.nlm.nih.gov/ It is also distributed on the EMBL CD-ROMs. The home page for PRINTS is: http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ Output file format Output files for usage example Directory: PRINTS This directory contains output files. The output files are held in the PRINTS subdirectory of the EMBOSS data directory. * prints.mat matrices calculated from PRINTS * Pxxxxx text information for each fingerprint Data files None. Notes You may have to ask your system manager to run this program. References 1. Attwood, T.K., Flower, D.R., Lewis, A.P., Mabey, J.E., Morgan, S.R., Scordis, P., Selley, J. and Wright, W. (1999) PRINTS prepares for the new millennium. Nucleic Acids Research, 27(1), 220-225. 2. Attwood, T.K., Beck, M.E., Flower, D.R., Scordis, P. and Selley, J. (1998) The PRINTS protein fingerprint database in its fifth year. Nucleic Acids Research, 26(1), 304-308. 3. Attwood, T.K., Beck, M.E., Bleasby, A.J., Degtyarenko, K., Michie, A.D. and Parry-Smith, D.J. (1997) Novel developments with the PRINTS protein motif fingerprint database. Nucleic Acids Research, 25 (1), 212-216. 4. Attwood, T.K. and Beck, M.E. (1994) PRINTS - A protein motif fingerprint database. Protein Engineering, 7(7), 841-848. 5. Bleasby, A.J., Akrigg, D.A. and Attwood, T.K. (1994) OWL - A non-redundant composite protein sequence database. Nucleic Acids Research, 22(17), 3574-77. 6. Bleasby, A.J. and Wootton, J.C. (1990) Constructing validated, non- redundant composite protein sequence databases. Protein Engineering, 3(3), 153-159. 7. Parry-Smith, D.J. and Attwood, T.K. (1992) ADSP - A new package for computational sequence analysis. CABIOS, 8(5), 451-459. 8. Attwood, T.K. and Findlay, J.B.C. (1994) Fingerprinting G-protein-coupled receptors. Prot.Engng. 7(2), 195-203. 9. Attwood, T.K. and Findlay, J.B.C. (1993) Design of a discriminating finger- print for G-protein-coupled receptors. Prot.Engng. 6(2) 167-176. 10. Akrigg, D., Attwood, T.K., Bleasby, A.J., Findlay, J.B.C, North, A.C.T., Maughan, N.A., Parry-Smith, D.J., Perkins, D.N. and Wootton, J.C. (1992) SERPENT - An information storage and analysis resource for protein sequences. CABIOS 8(3) 295-296. 11. Parry-Smith, D.J. and Attwood, T.K. (1991) SOMAP - A novel interactive approach to multiple protein sequence aligment. CABIOS, 7(2), 233-235. 12. Perkins, D.N. and Attwood, T.K. (1995) VISTAS - A package for VIsualising STructures And Sequences of proteins. J.Mol.Graph., 13, 73-75. 13. Parry-Smith, D.J., Payne, A.W.R, Michie, A.D. and Attwood, T.K. (1998) CINEMA - A novel Colour INteractive Editor for Multiple Alignments. Gene, 211(2), GC45-56. Warnings The program will warn you if the input file is incorrectly formatted. If you do not have write-access to the EMBOSS data directory, you should ask your system manager to run this program. Diagnostic Error Messages None. Exit status It exits with status 0 unless an error is reported. Known bugs None. See also Program name Description aaindexextract Extract amino acid property data from AAINDEX cutgextract Extract codon usage tables from CUTG database jaspextract Extract data from JASPAR prosextract Processes the PROSITE motif database for use by patmatmotifs rebaseextract Process the REBASE database for use by restriction enzyme applications tfextract Process TRANSFAC transcription factor database for use by tfscan Author(s) Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Completed 8th April 1999 Target users This program is intended to be used by administrators responsible for software and database installation and maintenance. Comments None