From 372bf55827f78fe32167162f7af6eca2ab86c7c4 Mon Sep 17 00:00:00 2001 From: jason Date: Tue, 28 Oct 2008 17:26:48 +0000 Subject: [PATCH] jasonfail. add missing test data file for FASTA v35.04 svn path=/bioperl-live/trunk/; revision=14972 --- t/data/BOSS_DROME.FASTP_v35_04 | 119 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 t/data/BOSS_DROME.FASTP_v35_04 diff --git a/t/data/BOSS_DROME.FASTP_v35_04 b/t/data/BOSS_DROME.FASTP_v35_04 new file mode 100644 index 000000000..7e771f7be --- /dev/null +++ b/t/data/BOSS_DROME.FASTP_v35_04 @@ -0,0 +1,119 @@ +# fasta35 -E 1 -H BOSS_DROME.fa wormpep190 +FASTA searches a protein or DNA sequence data bank + version 35.04 Aug. 28, 2008 +Please cite: + W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 + +Query: BOSS_DROME.fa + 1>>>BOSS_DROME Protein bride of sevenless precursor. - 896 aa +Library: wormpep190 10449259 residues in 23771 sequences + +10449259 residues in 23771 sequences +Statistics: Expectation_n fit: rho(ln(x))= 5.6522+/-0.000443; mu= 12.7762+/- 0.026 + mean_var=109.3856+/-23.016, 0's: 1 Z-trim: 2 B-trim: 0 in 0/59 + Lambda= 0.122629 +Algorithm: FASTA (3.5 Sept 2006) [optimized] +Parameters: BL50 matrix (15:-5) ktup: 2 + join: 38, opt: 26, open/ext: -10/-2, width: 16 + Scan time: 2.980 + +The best scores are: opt bits E(23771) +F35H10.10 CE24945 WBGene00018073 status:Confirmed (1404) 207 48.2 9.2e-05 + +>>F35H10.10 CE24945 WBGene00018073 status:Confirmed UniP (1404 aa) + initn: 94 init1: 94 opt: 207 Z-score: 196.5 bits: 48.2 E(): 9.2e-05 +Smith-Waterman score: 275; 22.7% identity (52.3% similar) in 728 aa overlap (207-847:640-1330) + + 180 190 200 210 220 230 +BOSS_D RAISIDNASLAENLLIQEVQFLQQCTTYSMGIFVDWELYKQLESVIKD---LEYNIWPIP + : : . . .: :: .. :. .. .: +F35H10 NQAGRNITIVPKSVFGYASALHGDSQESLKGYFSSGDTDASLVSVDSEHSALQRSFTALP + 610 620 630 640 650 660 + + 240 250 260 270 280 +BOSS_D GTRAHLFPKVAHLLHQMPWGEKIASV-EIATETLEMYNEFMEAARQEHMCLM-------- + ..: . . . .::..: : :.. : :.: .. : . : .. .:: +F35H10 SSRNQALA-LLKLLNRMQWQFVTAALSEQDPESLSLFRAFERLALDRGVCLAEVLNIGGS + 670 680 690 700 710 720 + + 290 300 310 320 330 +BOSS_D ---HFKSDDNVYIMFGN-KLASHF----KENGTLFSVPTDRTDDEFLAD------LPNRA + ...: :: :.:.. . :. . : :. .: .. : .: .:. . +F35H10 RLDNIRSTTNVTIVFSTARDAADYLIASKIRGNHVNVMMGEAHDWYLHAPNNKELFPGTV + 730 740 750 760 770 780 + + 340 350 360 370 +BOSS_D FVLMENEI--DLSTAVELDATPTALDEILIGKSVLPSR---VLSFAGSII--------DL + : .: . :. .: .:: .: : : : . :: .:: ...: .: +F35H10 SVQPRNILYGDFREWLET-TTPLTLPE-LWYWSYIESRYGCALSQKSKVIYGKMCTGDEL + 790 800 810 820 830 840 + + 380 390 400 410 420 430 +BOSS_D MNWLR-GSLSK--HCKRGEEHDLYVLESCFNFLNFIEDWRTSEYRQAHDTAEILSLLLMR + .: : ..: . .:: :. :....: .. : .. :. . . .::. : . +F35H10 LNIESLGRMTKAGYLSRGVERFLFAMDSVYKSLCPAQNGLCLEFYE-QGRRQILTQL--K + 850 860 870 880 890 900 + + 440 450 460 470 480 490 +BOSS_D KLGTAMNFQMYQKKVLTLDKITGESRTELREIASQNFVTNVTTYYHYNRDNHTSLELKTK + : .: . ..:. : :... .: ::. ...:.. .: : . : : . +F35H10 KTSTEDDVEIYE----FLPDINNHFTYHL--IANWTLTTGLRMTNQYRNGNGVPTESKCQ + 910 920 930 940 950 + + 500 510 520 +BOSS_D -----------FGQ------VFNCQYSAGDN-----RRYPFLFDGESV----MFWRIKMD + : : :: . :.. .: : : .:.. .: .: +F35H10 PPMCKCFLDGDFFQRPLDSFVFRPDEPEGSDQSSYIKRQP-AFGSEKIEYQSVFEHITTG + 960 970 980 990 1000 1010 + + 530 540 550 560 570 580 +BOSS_D TWVATGLTAAILGLIATL-----AILVFIVVRISLGDVFEGNPTTSILLLLSLILVFCSF + : . ..:.::..: :.::...:.. : : .:: . .: ::...:.. +F35H10 HWRDHPHNYVLLALITVLVVVAIAVLVLVLVKLYL-RVVKGNQSLGISLLIGIIIL---- + 1020 1030 1040 1050 1060 1070 + + 590 600 610 620 630 640 +BOSS_D VPYSIEYVGEQRNSHVTFEDAQTLNTLCAVRVFIMTLVYCFVFSLLLCRAVMLASIGSEG + :: . .:. . ...: .::.. : : . :.... .:..: . . : +F35H10 --YSTAFF-------FVFDPT---DSVCRLRVILHGLGYTICFGVMIAKATQLRNAETLG + 1080 1090 1100 1110 + + 650 660 670 680 690 +BOSS_D -GFLSHVNGYIQAVICAFSVVAQVGMSVQLLVVMHVASETVSCENIY-----YGRWLWGL + : :.. . .. : : .:...:.. .. ... : :. .:. . . +F35H10 FGTAIHISFWNYWLLLFFIVGVQIALSISWFLEPFMSTIGVIDTNVQRMMCTMGKVEFVV + 1120 1130 1140 1150 1160 1170 + + 700 710 720 730 740 750 +BOSS_D LAYDFALLCCVGALIPSIYRS-QRNYREGILIVIGSVLIMVIWVAWIALSLFGD-EWRDA + . .: .. .: . :. .:::.: .. ..:: . :::::.: : : :.::. +F35H10 SNFYVMILIFMALFISMLNRNIKRNYKETKWLLYSTVLCFFTWVAWITLYLVLDHEFRDT + 1180 1190 1200 1210 1220 1230 + + 760 770 780 790 800 810 +BOSS_D AIPLGLQASGWAVLVGILI-PRTFLIVRGIERSDIA---QALPSLTSLAFAQNNQYSSEQ + .: . : : . ..:.:.:. :. .... . : .: . .:. :.: : .... :.. +F35H10 VIVVELVACA-TILLGFLFGPKIYILL-SYEPVVVAFKRDPFPNHTDL-FEKDDDLPSQR + 1240 1250 1260 1270 1280 1290 + + 820 830 840 850 860 +BOSS_D SVYECVNPAMRHCSQDEVNHQSPSEIPTL--PLRGGGPRRQQFFANLRQANANINPQRPP + . :.:: :... . .. : . :. . :: +F35H10 A----VSPASSTSSSSNRSSSGSSYTSSSKRPVNAVGPLPLNKNVEDQSPIFHTVMRKKT + 1300 1310 1320 1330 1340 1350 + + 870 880 890 +BOSS_D PRPQQSPSRSSVSSLPPSPDHNKITRF + +F35H10 KVRRSNSEHDTIMNVGIPMTSVPIIRSPSARDEKVHRVAISPPIRDYNSINH + 1360 1370 1380 1390 1400 + + + +896 residues in 1 query sequences +10449259 residues in 23771 library sequences + Scomplib [35.04] + start: Wed Oct 22 20:59:06 2008 done: Wed Oct 22 20:59:09 2008 + Total Scan time: 2.980 Total Display time: 0.030 + +Function used was FASTA [version 35.04 Aug. 28, 2008] -- 2.11.4.GIT