------------------------------------------------------------ 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 24 sequences from file BOMBESIN PATTERN CONSERVATION: CM: min Nr of Seqs to Match 24 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 BOMBESIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ALYT_ALYOB 14 BOMB_BOMOR 119 BOMB_BOMVA 107 BOML_PSEGU 13 GRP1_HUMAN 138 GRP2_HUMAN 148 GRP_ALLMI 28 GRP_BOMOR 155 GRP_CANFA 27 GRP_CHICK 27 GRP_PIG 27 GRP_RANRI 10 GRP_RAT 147 GRP_SCYCA 25 LITL_PHYSA 9 LITO_LITAU 9 LITP_PHYSA 9 LITR_PHYRO 9 NEUB_HUMAN 76 NEUB_PIG 32 NEUM_XENLA 120 RANA_RANPI 82 RANC_RANPI 11 RANR_RANRU 17 Pratt run started at Thu Feb 6 18:59:57 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.6802 24( 24) W-A-x-G-x(2)-M 2: 12.5102 25( 24) A-x-G-x(2)-M 3: 8.3401 25( 24) G-x(2)-M Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 19.9482 24( 24) W-A-x-G-x-[FL]-M B 2: 15.7782 24( 24) A-x-G-x-[FL]-M C 3: 11.6081 24( 24) G-x-[FL]-M Best patterns with alignements: fitness hits(seqs) Pattern A 1: 19.9482 24( 24) W-A-x-G-x-[FL]-M Occurences: 24(24) ALYT_ALYOB : 8- 14: rlgtq WAvGhLM BOMB_BOMOR : 52- 58: rlgnq WAvGhLM gkksl BOMB_BOMVA : 49- 55: rlgnq WAvGhLM gkksl BOML_PSEGU : 7- 13: gggpq WAvGhFM GRP1_HUMAN : 44- 50: prgnh WAvGhLM gkkst GRP2_HUMAN : 44- 50: prgnh WAvGhLM gkkst GRP_ALLMI : 22- 28: prgsh WAvGhLM GRP_BOMOR : 54- 60: prgsh WAvGhLM gkksi GRP_CANFA : 21- 27: prgnh WAvGhLM GRP_CHICK : 21- 27: prgsh WAvGhLM GRP_PIG : 21- 27: prgnh WAvGhLM GRP_RANRI : 4- 10: gsh WAvGhLM GRP_RAT : 46- 52: prgsh WAvGhLM gkkst GRP_SCYCA : 19- 25: prgsh WAvGhLM LITL_PHYSA : 3- 9: ql WAvGsLM LITO_LITAU : 3- 9: qq WAvGhFM LITP_PHYSA : 3- 9: ql WAvGsFM LITR_PHYRO : 3- 9: ql WAtGhFM NEUB_HUMAN : 50- 56: srgnl WAtGhFM gkksl NEUB_PIG : 26- 32: prgnl WAtGhFM NEUM_XENLA : 48- 54: rrgnq WAiGhFM gkksl RANA_RANPI : 52- 58: rqvpq WAvGhFM gkrsl RANC_RANPI : 5- 11: ztpq WAtGhFM RANR_RANRU : 11- 17: rrynq WAtGhFM B 2: 15.7782 24( 24) A-x-G-x-[FL]-M Occurences: 24(24) ALYT_ALYOB : 9- 14: lgtqw AvGhLM BOMB_BOMOR : 53- 58: lgnqw AvGhLM gkksl BOMB_BOMVA : 50- 55: lgnqw AvGhLM gkksl BOML_PSEGU : 8- 13: ggpqw AvGhFM GRP1_HUMAN : 45- 50: rgnhw AvGhLM gkkst GRP2_HUMAN : 45- 50: rgnhw AvGhLM gkkst GRP_ALLMI : 23- 28: rgshw AvGhLM GRP_BOMOR : 55- 60: rgshw AvGhLM gkksi GRP_CANFA : 22- 27: rgnhw AvGhLM GRP_CHICK : 22- 27: rgshw AvGhLM GRP_PIG : 22- 27: rgnhw AvGhLM GRP_RANRI : 5- 10: gshw AvGhLM GRP_RAT : 47- 52: rgshw AvGhLM gkkst GRP_SCYCA : 20- 25: rgshw AvGhLM LITL_PHYSA : 4- 9: qlw AvGsLM LITO_LITAU : 4- 9: qqw AvGhFM LITP_PHYSA : 4- 9: qlw AvGsFM LITR_PHYRO : 4- 9: qlw AtGhFM NEUB_HUMAN : 51- 56: rgnlw AtGhFM gkksl NEUB_PIG : 27- 32: rgnlw AtGhFM NEUM_XENLA : 49- 54: rgnqw AiGhFM gkksl RANA_RANPI : 53- 58: qvpqw AvGhFM gkrsl RANC_RANPI : 6- 11: ztpqw AtGhFM RANR_RANRU : 12- 17: rynqw AtGhFM C 3: 11.6081 24( 24) G-x-[FL]-M Occurences: 24(24) ALYT_ALYOB : 11- 14: tqwav GhLM BOMB_BOMOR : 55- 58: nqwav GhLM gkksl BOMB_BOMVA : 52- 55: nqwav GhLM gkksl BOML_PSEGU : 10- 13: pqwav GhFM GRP1_HUMAN : 47- 50: nhwav GhLM gkkst GRP2_HUMAN : 47- 50: nhwav GhLM gkkst GRP_ALLMI : 25- 28: shwav GhLM GRP_BOMOR : 57- 60: shwav GhLM gkksi GRP_CANFA : 24- 27: nhwav GhLM GRP_CHICK : 24- 27: shwav GhLM GRP_PIG : 24- 27: nhwav GhLM GRP_RANRI : 7- 10: shwav GhLM GRP_RAT : 49- 52: shwav GhLM gkkst GRP_SCYCA : 22- 25: shwav GhLM LITL_PHYSA : 6- 9: qlwav GsLM LITO_LITAU : 6- 9: qqwav GhFM LITP_PHYSA : 6- 9: qlwav GsFM LITR_PHYRO : 6- 9: qlwat GhFM NEUB_HUMAN : 53- 56: nlwat GhFM gkksl NEUB_PIG : 29- 32: nlwat GhFM NEUM_XENLA : 51- 54: nqwai GhFM gkksl RANA_RANPI : 55- 58: pqwav GhFM gkrsl RANC_RANPI : 8- 11: pqwat GhFM RANR_RANRU : 14- 17: nqwat GhFM Number of patterns evaluated by Pratt:6 Total running time: 1 seconds