------------------------------------------------------------ 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 9 sequences from file UROTENSIN_II PATTERN CONSERVATION: CM: min Nr of Seqs to Match 9 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 UROTENSIN_II.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: UR2A_CATCO 12 UR2A_CYPCA 125 UR2B_CATCO 12 UR2B_CYPCA 12 UR2G_CYPCA 125 UR2_GILMI 12 UR2_PLAFE 83 UR2_RANRI 13 UR2_SCYCA 12 Pratt run started at Thu Feb 6 21:32:27 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 25.0203 9( 9) C-F-W-K-Y-C 2: 20.8503 9( 9) F-W-K-Y-C 3: 16.6802 9( 9) W-K-Y-C 4: 12.5102 9( 9) K-Y-C 5: 8.3401 9( 9) Y-C 6: 7.8401 9( 9) C-x(0,1)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 28.2452 9( 9) C-F-W-K-Y-C-[IV] B 2: 24.0751 9( 9) F-W-K-Y-C-[IV] C 3: 19.9051 9( 9) W-K-Y-C-[IV] D 4: 15.7350 9( 9) K-Y-C-[IV] E 5: 11.5650 9( 9) Y-C-[IV] F 6: 7.8401 9( 9) C-x(0,1)-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 28.2452 9( 9) C-F-W-K-Y-C-[IV] Occurences: 9(9) UR2A_CATCO : 6- 12: gsgad CFWKYCV UR2A_CYPCA : 119- 125: gggad CFWKYCV UR2B_CATCO : 6- 12: gsnte CFWKYCV UR2B_CYPCA : 6- 12: ggnte CFWKYCV UR2G_CYPCA : 119- 125: gggad CFWKYCI UR2_GILMI : 6- 12: agtad CFWKYCV UR2_PLAFE : 77- 83: agtte CFWKYCV UR2_RANRI : 7- 13: gnlse CFWKYCV UR2_SCYCA : 6- 12: nnfsd CFWKYCV B 2: 24.0751 9( 9) F-W-K-Y-C-[IV] Occurences: 9(9) UR2A_CATCO : 7- 12: sgadc FWKYCV UR2A_CYPCA : 120- 125: ggadc FWKYCV UR2B_CATCO : 7- 12: sntec FWKYCV UR2B_CYPCA : 7- 12: gntec FWKYCV UR2G_CYPCA : 120- 125: ggadc FWKYCI UR2_GILMI : 7- 12: gtadc FWKYCV UR2_PLAFE : 78- 83: gttec FWKYCV UR2_RANRI : 8- 13: nlsec FWKYCV UR2_SCYCA : 7- 12: nfsdc FWKYCV C 3: 19.9051 9( 9) W-K-Y-C-[IV] Occurences: 9(9) UR2A_CATCO : 8- 12: gadcf WKYCV UR2A_CYPCA : 121- 125: gadcf WKYCV UR2B_CATCO : 8- 12: ntecf WKYCV UR2B_CYPCA : 8- 12: ntecf WKYCV UR2G_CYPCA : 121- 125: gadcf WKYCI UR2_GILMI : 8- 12: tadcf WKYCV UR2_PLAFE : 79- 83: ttecf WKYCV UR2_RANRI : 9- 13: lsecf WKYCV UR2_SCYCA : 8- 12: fsdcf WKYCV D 4: 15.7350 9( 9) K-Y-C-[IV] Occurences: 9(9) UR2A_CATCO : 9- 12: adcfw KYCV UR2A_CYPCA : 122- 125: adcfw KYCV UR2B_CATCO : 9- 12: tecfw KYCV UR2B_CYPCA : 9- 12: tecfw KYCV UR2G_CYPCA : 122- 125: adcfw KYCI UR2_GILMI : 9- 12: adcfw KYCV UR2_PLAFE : 80- 83: tecfw KYCV UR2_RANRI : 10- 13: secfw KYCV UR2_SCYCA : 9- 12: sdcfw KYCV E 5: 11.5650 9( 9) Y-C-[IV] Occurences: 9(9) UR2A_CATCO : 10- 12: dcfwk YCV UR2A_CYPCA : 123- 125: dcfwk YCV UR2B_CATCO : 10- 12: ecfwk YCV UR2B_CYPCA : 10- 12: ecfwk YCV UR2G_CYPCA : 123- 125: dcfwk YCI UR2_GILMI : 10- 12: dcfwk YCV UR2_PLAFE : 81- 83: ecfwk YCV UR2_RANRI : 11- 13: ecfwk YCV UR2_SCYCA : 10- 12: dcfwk YCV F 6: 7.8401 9( 9) C-x(0,1)-V Occurences: 9(9) UR2A_CATCO : 11- 12: cfwky C-V UR2A_CYPCA : 124- 125: cfwky C-V UR2B_CATCO : 11- 12: cfwky C-V UR2B_CYPCA : 11- 12: cfwky C-V UR2G_CYPCA : 9- 11: nllls CsV lllsc UR2_GILMI : 11- 12: cfwky C-V UR2_PLAFE : 82- 83: cfwky C-V UR2_RANRI : 12- 13: cfwky C-V UR2_SCYCA : 11- 12: cfwky C-V Number of patterns evaluated by Pratt:16 Total running time: 0 seconds