------------------------------------------------------------ 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 7 sequences from file NMU PATTERN CONSERVATION: CM: min Nr of Seqs to Match 7 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 NMU.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: NEUU_CANFA 25 NEUU_CAVPO 9 NEUU_CHICK 25 NEUU_PIG 25 NEUU_RABIT 25 NEUU_RANTE 25 NEUU_RAT 174 Pratt run started at Thu Feb 6 20:25:18 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 25.0203 7( 7) F-x-F-R-P-R-N 2: 20.8503 7( 7) F-R-P-R-N 3: 16.6802 7( 7) R-P-R-N 4: 12.5102 7( 7) P-R-N 5: 8.3401 7( 7) R-N Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 27.6702 7( 7) F-[FLV]-F-R-P-R-N B 2: 20.8503 7( 7) F-R-P-R-N C 3: 16.6802 7( 7) R-P-R-N D 4: 12.5102 7( 7) P-R-N E 5: 8.3401 7( 7) R-N Best patterns with alignements: fitness hits(seqs) Pattern A 1: 27.6702 7( 7) F-[FLV]-F-R-P-R-N Occurences: 7(7) NEUU_CANFA : 19- 25: qvrrq FLFRPRN NEUU_CAVPO : 3- 9: gy FLFRPRN NEUU_CHICK : 19- 25: qsrgy FFFRPRN NEUU_PIG : 19- 25: qnrry FLFRPRN NEUU_RABIT : 19- 25: rsrgy FLFRPRN NEUU_RANTE : 19- 25: lsrgy FVFRPRN NEUU_RAT : 160- 166: psggf FLFRPRN gkrst B 2: 20.8503 7( 7) F-R-P-R-N Occurences: 7(7) NEUU_CANFA : 21- 25: rrqfl FRPRN NEUU_CAVPO : 5- 9: gyfl FRPRN NEUU_CHICK : 21- 25: rgyff FRPRN NEUU_PIG : 21- 25: rryfl FRPRN NEUU_RABIT : 21- 25: rgyfl FRPRN NEUU_RANTE : 21- 25: rgyfv FRPRN NEUU_RAT : 162- 166: ggffl FRPRN gkrst C 3: 16.6802 7( 7) R-P-R-N Occurences: 7(7) NEUU_CANFA : 22- 25: rqflf RPRN NEUU_CAVPO : 6- 9: gyflf RPRN NEUU_CHICK : 22- 25: gyfff RPRN NEUU_PIG : 22- 25: ryflf RPRN NEUU_RABIT : 22- 25: gyflf RPRN NEUU_RANTE : 22- 25: gyfvf RPRN NEUU_RAT : 163- 166: gfflf RPRN gkrst D 4: 12.5102 7( 7) P-R-N Occurences: 7(7) NEUU_CANFA : 23- 25: qflfr PRN NEUU_CAVPO : 7- 9: yflfr PRN NEUU_CHICK : 23- 25: yfffr PRN NEUU_PIG : 23- 25: yflfr PRN NEUU_RABIT : 23- 25: yflfr PRN NEUU_RANTE : 23- 25: yfvfr PRN NEUU_RAT : 164- 166: fflfr PRN gkrst E 5: 8.3401 7( 7) R-N Occurences: 7(7) NEUU_CANFA : 24- 25: flfrp RN NEUU_CAVPO : 8- 9: flfrp RN NEUU_CHICK : 24- 25: fffrp RN NEUU_PIG : 24- 25: flfrp RN NEUU_RABIT : 24- 25: flfrp RN NEUU_RANTE : 24- 25: fvfrp RN NEUU_RAT : 165- 166: flfrp RN gkrst Number of patterns evaluated by Pratt:15 Total running time: 0 seconds