------------------------------------------------------------ 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 13 sequences from file PHOTOSYSTEM_I_PSAGK PATTERN CONSERVATION: CM: min Nr of Seqs to Match 13 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 PHOTOSYSTEM_I_PSAGK.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: PSAG_CHLRE 126 PSAG_CUCSA 14 PSAG_HORVU 143 PSAG_PEA 39 PSAG_SPIOL 167 PSAK_ANAVA 31 PSAK_CHLRE 113 PSAK_CUCSA 33 PSAK_HORVU 131 PSAK_PEA 20 PSAK_SPIOL 29 PSAK_SYNEN 83 PSAK_SYNVU 85 Pratt run started at Thu Feb 6 20:39:57 1997 No patterns found