------------------------------------------------------------ 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 18 sequences from file GNRH PATTERN CONSERVATION: CM: min Nr of Seqs to Match 18 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 GNRH.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: GON1_ALLMI 10 GON1_CHICK 92 GON1_CLAGA 80 GON1_HAPBU 90 GON1_ONCMA 82 GON1_PETMA 10 GON1_SALSA 82 GON1_SALTR 82 GON1_SQUAC 10 GON1_XENLA 89 GON2_CHICK 10 GON2_CLAGA 86 GON2_HAPBU 85 GON3_PETMA 10 GONL_HUMAN 92 GONL_MOUSE 90 GONL_ONCKE 10 GONL_RAT 92 Pratt run started at Thu Feb 6 19:42:17 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.8503 18( 18) Q-H-x-S-x(4)-P-G 2: 16.6802 18( 18) H-x-S-x(4)-P-G 3: 12.5102 18( 18) S-x(4)-P-G 4: 8.3401 20( 18) P-G 5: 8.3401 28( 18) W-x(2)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 26.8447 18( 18) Q-H-[WY]-S-x-[DEG]-x(2)-P-G B 2: 22.6747 18( 18) H-[WY]-S-x-[DEG]-x(2)-P-G C 3: 15.1607 18( 18) S-x-[DEG]-x(2)-P-G D 4: 8.3401 20( 18) P-G E 5: 8.3401 28( 18) W-x(2)-G Best patterns with alignements: fitness hits(seqs) Pattern A 1: 26.8447 18( 18) Q-H-[WY]-S-x-[DEG]-x(2)-P-G Occurences: 18(18) GON1_ALLMI : 1- 10: QHWSyGlqPG GON1_CHICK : 24- 33: aicla QHWSyGlqPG gkrna GON1_CLAGA : 22- 31: lqvsa QHWShGlnPG gkrav GON1_HAPBU : 24- 33: qvtls QHWSyGwlPG gkrsv GON1_ONCMA : 24- 33: qvtfs QHWSyGwlPG gkrsv GON1_PETMA : 1- 10: QHYSlEwkPG GON1_SALSA : 24- 33: qvtls QHWSyGwlPG gkrsv GON1_SALTR : 24- 33: qvtls QHWSyGwlPG gkrsv GON1_SQUAC : 1- 10: QHWShGwlPG GON1_XENLA : 24- 33: hvsda QHWSyGlrPG gkrdt GON2_CHICK : 1- 10: QHWShGwyPG GON2_CLAGA : 25- 34: qlsfs QHWShGwyPG gkrei GON2_HAPBU : 24- 33: qlsfa QHWShGwyPG gkrel GON3_PETMA : 1- 10: QHWShDwkPG GONL_HUMAN : 24- 33: egcss QHWSyGlrPG gkrda GONL_MOUSE : 22- 31: egcss QHWSyGlrPG gkrnt GONL_ONCKE : 1- 10: QHWSyGwlPG GONL_RAT : 24- 33: egcss QHWSyGlrPG gkrnt B 2: 22.6747 18( 18) H-[WY]-S-x-[DEG]-x(2)-P-G Occurences: 18(18) GON1_ALLMI : 2- 10: q HWSyGlqPG GON1_CHICK : 25- 33: iclaq HWSyGlqPG gkrna GON1_CLAGA : 23- 31: qvsaq HWShGlnPG gkrav GON1_HAPBU : 25- 33: vtlsq HWSyGwlPG gkrsv GON1_ONCMA : 25- 33: vtfsq HWSyGwlPG gkrsv GON1_PETMA : 2- 10: q HYSlEwkPG GON1_SALSA : 25- 33: vtlsq HWSyGwlPG gkrsv GON1_SALTR : 25- 33: vtlsq HWSyGwlPG gkrsv GON1_SQUAC : 2- 10: q HWShGwlPG GON1_XENLA : 25- 33: vsdaq HWSyGlrPG gkrdt GON2_CHICK : 2- 10: q HWShGwyPG GON2_CLAGA : 26- 34: lsfsq HWShGwyPG gkrei GON2_HAPBU : 25- 33: lsfaq HWShGwyPG gkrel GON3_PETMA : 2- 10: q HWShDwkPG GONL_HUMAN : 25- 33: gcssq HWSyGlrPG gkrda GONL_MOUSE : 23- 31: gcssq HWSyGlrPG gkrnt GONL_ONCKE : 2- 10: q HWSyGwlPG GONL_RAT : 25- 33: gcssq HWSyGlrPG gkrnt C 3: 15.1607 18( 18) S-x-[DEG]-x(2)-P-G Occurences: 18(18) GON1_ALLMI : 4- 10: qhw SyGlqPG GON1_CHICK : 27- 33: laqhw SyGlqPG gkrna GON1_CLAGA : 25- 31: saqhw ShGlnPG gkrav GON1_HAPBU : 27- 33: lsqhw SyGwlPG gkrsv GON1_ONCMA : 27- 33: fsqhw SyGwlPG gkrsv GON1_PETMA : 4- 10: qhy SlEwkPG GON1_SALSA : 27- 33: lsqhw SyGwlPG gkrsv GON1_SALTR : 27- 33: lsqhw SyGwlPG gkrsv GON1_SQUAC : 4- 10: qhw ShGwlPG GON1_XENLA : 27- 33: daqhw SyGlrPG gkrdt GON2_CHICK : 4- 10: qhw ShGwyPG GON2_CLAGA : 28- 34: fsqhw ShGwyPG gkrei GON2_HAPBU : 27- 33: faqhw ShGwyPG gkrel GON3_PETMA : 4- 10: qhw ShDwkPG GONL_HUMAN : 27- 33: ssqhw SyGlrPG gkrda GONL_MOUSE : 25- 31: ssqhw SyGlrPG gkrnt GONL_ONCKE : 4- 10: qhw SyGwlPG GONL_RAT : 27- 33: ssqhw SyGlrPG gkrnt D 4: 8.3401 20( 18) P-G Occurences: 20(18) GON1_ALLMI : 9- 10: syglq PG GON1_CHICK : 32- 33: syglq PG gkrna GON1_CHICK : 64- 65: qkaec PG syqhp GON1_CLAGA : 30- 31: shgln PG gkrav GON1_CLAGA : 59- 60: yvavs PG nkpfr GON1_HAPBU : 32- 33: sygwl PG gkrsv GON1_ONCMA : 32- 33: sygwl PG gkrsv GON1_PETMA : 9- 10: slewk PG GON1_SALSA : 32- 33: sygwl PG gkrsv GON1_SALTR : 32- 33: sygwl PG gkrsv GON1_SQUAC : 9- 10: shgwl PG GON1_XENLA : 32- 33: syglr PG gkrdt GON2_CHICK : 9- 10: shgwy PG GON2_CLAGA : 33- 34: shgwy PG gkrei GON2_HAPBU : 32- 33: shgwy PG gkrel GON3_PETMA : 9- 10: shdwk PG GONL_HUMAN : 32- 33: syglr PG gkrda GONL_MOUSE : 30- 31: syglr PG gkrnt GONL_ONCKE : 9- 10: sygwl PG GONL_RAT : 32- 33: syglr PG gkrnt E 5: 8.3401 28( 18) W-x(2)-G Occurences: 28(18) GON1_ALLMI : 3- 6: qh WsyG lqpg GON1_CHICK : 26- 29: claqh WsyG lqpgg GON1_CLAGA : 24- 27: vsaqh WshG lnpgg GON1_HAPBU : 26- 29: tlsqh WsyG wlpgg GON1_HAPBU : 30- 33: hwsyg WlpG gkrsv GON1_ONCMA : 26- 29: tfsqh WsyG wlpgg GON1_ONCMA : 30- 33: hwsyg WlpG gkrsv GON1_PETMA : 7- 10: hysle WkpG GON1_SALSA : 26- 29: tlsqh WsyG wlpgg GON1_SALSA : 30- 33: hwsyg WlpG gkrsv GON1_SALTR : 26- 29: tlsqh WsyG wlpgg GON1_SALTR : 30- 33: hwsyg WlpG gkrsv GON1_SQUAC : 3- 6: qh WshG wlpg GON1_SQUAC : 7- 10: hwshg WlpG GON1_XENLA : 26- 29: sdaqh WsyG lrpgg GON1_XENLA : 80- 83: galmn WleG enrkk GON2_CHICK : 3- 6: qh WshG wypg GON2_CHICK : 7- 10: hwshg WypG GON2_CLAGA : 27- 30: sfsqh WshG wypgg GON2_CLAGA : 31- 34: hwshg WypG gkrei GON2_HAPBU : 26- 29: sfaqh WshG wypgg GON2_HAPBU : 30- 33: hwshg WypG gkrel GON3_PETMA : 7- 10: hwshd WkpG GONL_HUMAN : 26- 29: cssqh WsyG lrpgg GONL_MOUSE : 24- 27: cssqh WsyG lrpgg GONL_ONCKE : 3- 6: qh WsyG wlpg GONL_ONCKE : 7- 10: hwsyg WlpG GONL_RAT : 26- 29: cssqh WsyG lrpgg Number of patterns evaluated by Pratt:11 Total running time: 0 seconds