------------------------------------------------------------ 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 36 sequences from file GASTRIN PATTERN CONSERVATION: CM: min Nr of Seqs to Match 36 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 GASTRIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ANTR_CHICK 53 ANTR_PSESC 52 ANTR_RANCA 47 CAE1_XENLA 188 CAE2_XENLA 136 CAE3_XENLA 169 CAE4_XENBO 234 CAE4_XENLA 233 CAE5_XENLA 187 CCKN_BOVIN 58 CCKN_HUMAN 115 CCKN_MACEU 8 CCKN_MACFA 115 CCKN_MOUSE 115 CCKN_PIG 114 CCKN_PSESC 70 CCKN_RANCA 69 CCKN_RAT 115 CION_CIOIN 128 DSK1_DROME 128 GAST_BOVIN 104 GAST_CANFA 34 GAST_CAPHI 34 GAST_CAVPO 33 GAST_CHIBR 33 GAST_DIDMA 33 GAST_FELCA 104 GAST_HUMAN 101 GAST_MACMU 17 GAST_PIG 104 GAST_RAT 104 LSK1_LEUMA 11 LSK2_LEUMA 10 LSKP_PERAM 11 NSK1_SARBU 9 NSK2_SARBU 14 Pratt run started at Thu Feb 6 19:32:17 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.8401 53( 36) M-x(0,1)-F Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.8401 53( 36) M-x(0,1)-F Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.8401 53( 36) M-x(0,1)-F Occurences: 53(36) ANTR_CHICK : 51- 53: fypdw MdF ANTR_PSESC : 50- 52: dypgw MdF ANTR_RANCA : 45- 47: dyagw MdF CAE1_XENLA : 1- 2: M-F kgill CAE1_XENLA : 178- 180: dytgw MdF grrng CAE2_XENLA : 1- 2: M-F kgill CAE3_XENLA : 1- 2: M-F kgill CAE3_XENLA : 80- 82: dytgw MdF grrdg CAE3_XENLA : 95- 97: dytgw MdF grrdd CAE3_XENLA : 159- 161: dytgw MdF grrng CAE4_XENBO : 1- 2: M-F kgill CAE4_XENBO : 81- 83: dytgw MdF grrdd CAE4_XENBO : 145- 147: dytgw MdF grrdg CAE4_XENBO : 160- 162: dytgw MdF grrdd CAE4_XENBO : 224- 226: dytgw MdF grrng CAE4_XENLA : 1- 2: M-F kgill CAE4_XENLA : 80- 82: dytgw MdF grrdg CAE4_XENLA : 95- 97: dytgw MdF grrdd CAE4_XENLA : 159- 161: dytgw MdF grrdd CAE4_XENLA : 223- 225: dytgw MdF grrng CAE5_XENLA : 17- 19: dytgw MdF grrdd CAE5_XENLA : 81- 83: dytgw MdF grrdd CAE5_XENLA : 145- 147: dytgw MdF grrdg CAE5_XENLA : 160- 162: dytgw MdF grrdd CCKN_BOVIN : 56- 58: dymgw MdF CCKN_HUMAN : 101- 103: dymgw MdF grrsa CCKN_MACEU : 6- 8: dymgw MdF CCKN_MACFA : 101- 103: dymgw MdF grrsa CCKN_MOUSE : 101- 103: dymgw MdF grrsa CCKN_PIG : 100- 102: dymgw MdF grrsa CCKN_PSESC : 68- 70: dymgw MdF CCKN_RANCA : 67- 69: dymgw MdF CCKN_RAT : 101- 103: dymgw MdF grrsa CION_CIOIN : 114- 116: nyygw MdF gkrai DSK1_DROME : 67- 69: rnqkt MsF grrvp DSK1_DROME : 107- 109: ddygh MrF gkrgg DSK1_DROME : 124- 126: ddygh MrF gr GAST_BOVIN : 90- 92: aaygw MdF grrsa GAST_CANFA : 32- 34: aaygw MdF GAST_CAPHI : 32- 34: aaygw MdF GAST_CAVPO : 31- 33: aaygw MdF GAST_CHIBR : 31- 33: aaygw MdF GAST_DIDMA : 31- 33: eaygw MdF GAST_FELCA : 90- 92: aaygw MdF grrsa GAST_HUMAN : 90- 92: eaygw MdF grrsa GAST_MACMU : 15- 17: aaygw MdF GAST_PIG : 90- 92: eaygw MdF grrsa GAST_RAT : 90- 92: eaygw MdF grrsa LSK1_LEUMA : 9- 11: edygh MrF LSK2_LEUMA : 8- 10: ddygh MrF LSKP_PERAM : 9- 11: ddygh MrF NSK1_SARBU : 7- 9: ddygh MrF NSK2_SARBU : 12- 14: ddygh MrF Number of patterns evaluated by Pratt:1 Total running time: 0 seconds