------------------------------------------------------------ Pratt version 2.1, Sept. 1996 Written by Inge Jonassen, University of Bergen Norway email: inge@ii.uib.no For more information, see http://www.ii.uib.no/~inge/Pratt.html ------------------------------------------------------------ Please quote: I.Jonassen, J.F.Collins, D.G.Higgins. Protein Science 1995;4(8):1587-1595. ------------------------------------------------------------ Pratt version 2.1 Analysing 11 sequences from file PYROKININ PATTERN CONSERVATION: CM: min Nr of Seqs to Match 11 C%: min Percentage Seqs to Match 100.0 PATTERN RESTRICTIONS : PP: pos in seq [off,complete,start] off PL: max Pattern Length 50 PN: max Nr of Pattern Symbols 50 PX: max Nr of consecutive x's 5 FN: max Nr of flexible spacers 2 FL: max Flexibility 2 FP: max Flex.Product 10 BI: Input Pattern Symbol File off BN: Nr of Pattern Symbols Initial Search 20 PATTERN SCORING: S: Scoring [info,mdl,tree,dist,ppv] info SEARCH PARAMETERS: G: Pattern Graph from [seq,al,query] seq E: Search Greediness 3 R: Pattern Refinement on RG: Generalise ambiguous symbols off OUTPUT: OF: Output Filename PYROKININ.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: LMT1_LOCMI 12 LMT2_LOCMI 8 LMT3_LOCMI 9 LMT4_LOCMI 13 LPK1_LOCMI 16 LPK2_LOCMI 10 LPK_LEUMA 8 PBAN_BOMMO 192 PBAN_HELZE 33 PBAN_LYMDI 33 PHPT_PSESE 18 Pratt run started at Thu Feb 6 20:56:37 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.6802 14( 11) F-x-P-R-L 2: 12.5102 14( 11) P-R-L 3: 8.3401 17( 11) R-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 19.2689 12( 11) F-[STV]-P-R-L B 2: 12.5102 14( 11) P-R-L C 3: 8.3401 17( 11) R-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 19.2689 12( 11) F-[STV]-P-R-L Occurences: 12(11) LMT1_LOCMI : 8- 12: vpaaq FSPRL LMT2_LOCMI : 4- 8: egd FTPRL LMT3_LOCMI : 5- 9: rqqp FVPRL LMT4_LOCMI : 9- 13: qngmp FSPRL LPK1_LOCMI : 12- 16: wpqqp FVPRL LPK2_LOCMI : 6- 10: qsvpt FTPRL LPK_LEUMA : 4- 8: qts FTPRL PBAN_BOMMO : 154- 158: srtry FSPRL grtms PBAN_BOMMO : 164- 168: grtms FSPRL grels PBAN_HELZE : 29- 33: srtky FSPRL PBAN_LYMDI : 29- 33: srnky FSPRL PHPT_PSESE : 14- 18: fenve FTPRL B 2: 12.5102 14( 11) P-R-L Occurences: 14(11) LMT1_LOCMI : 10- 12: aaqfs PRL LMT2_LOCMI : 6- 8: egdft PRL LMT3_LOCMI : 7- 9: qqpfv PRL LMT4_LOCMI : 11- 13: gmpfs PRL LPK1_LOCMI : 14- 16: qqpfv PRL LPK2_LOCMI : 8- 10: vptft PRL LPK_LEUMA : 6- 8: qtsft PRL PBAN_BOMMO : 45- 47: alwfg PRL gkrsm PBAN_BOMMO : 120- 122: slefi PRL grrls PBAN_BOMMO : 156- 158: tryfs PRL grtms PBAN_BOMMO : 166- 168: tmsfs PRL grels PBAN_HELZE : 31- 33: tkyfs PRL PBAN_LYMDI : 31- 33: nkyfs PRL PHPT_PSESE : 16- 18: nveft PRL C 3: 8.3401 17( 11) R-L Occurences: 17(11) LMT1_LOCMI : 11- 12: aqfsp RL LMT2_LOCMI : 7- 8: gdftp RL LMT3_LOCMI : 8- 9: qpfvp RL LMT4_LOCMI : 1- 2: RL hqngm LMT4_LOCMI : 12- 13: mpfsp RL LPK1_LOCMI : 15- 16: qpfvp RL LPK2_LOCMI : 9- 10: ptftp RL LPK_LEUMA : 7- 8: tsftp RL PBAN_BOMMO : 46- 47: lwfgp RL gkrsm PBAN_BOMMO : 65- 66: rqtfl RL leaad PBAN_BOMMO : 121- 122: lefip RL grrls PBAN_BOMMO : 125- 126: prlgr RL sedmp PBAN_BOMMO : 157- 158: ryfsp RL grtms PBAN_BOMMO : 167- 168: msfsp RL grels PBAN_HELZE : 32- 33: kyfsp RL PBAN_LYMDI : 32- 33: kyfsp RL PHPT_PSESE : 17- 18: veftp RL Number of patterns evaluated by Pratt:6 Total running time: 0 seconds