Mercurial > repos > iuc > hmmer_hmmbuild
diff test-data/MADE1.hmm @ 5:750269125dc9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
| author | iuc |
|---|---|
| date | Tue, 16 Jun 2020 05:38:16 -0400 |
| parents | d0875d3f6544 |
| children | dc8860ba75d1 |
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--- a/test-data/MADE1.hmm Mon Jun 11 15:52:17 2018 -0400 +++ b/test-data/MADE1.hmm Tue Jun 16 05:38:16 2020 -0400 @@ -1,268 +1,268 @@ -HMMER3/f [3.2 | June 2018] +HMMER3/f [3.3 | Nov 2019] NAME MADE1 ACC DF0000629.2 DESC MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon LENG 80 -MAXL 369 +MAXL 190 ALPH DNA RF yes MM no CONS yes CS no MAP yes -DATE Fri Jun 8 12:16:29 2018 +DATE Thu May 14 18:28:16 2020 NSEQ 1997 -EFFN 3.911818 +EFFN 4.772646 CKSUM 3015610723 GA 15.98 TC 32.00 NC 15.90 -STATS LOCAL MSV -8.5408 0.71858 -STATS LOCAL VITERBI -9.6095 0.71858 -STATS LOCAL FORWARD -3.4185 0.71858 +STATS LOCAL MSV -8.5015 0.71857 +STATS LOCAL VITERBI -9.4437 0.71857 +STATS LOCAL FORWARD -3.3601 0.71857 HMM A C G T m->m m->i m->d i->m i->i d->m d->d - COMPO 1.24273 1.59618 1.63103 1.16152 + COMPO 1.26505 1.57847 1.62734 1.15507 1.38629 1.38629 1.38629 1.38629 - 0.03960 3.94183 3.94183 1.46634 0.26236 0.00000 * - 1 2.69765 2.44396 2.81521 0.24089 1 t x - - + 0.03610 4.03273 4.03273 1.46634 0.26236 0.00000 * + 1 2.88347 2.59729 3.00766 0.19823 1 t x - - 1.38629 1.38629 1.38629 1.38629 - 0.03960 3.94183 3.94183 1.46634 0.26236 1.09861 0.40547 - 2 2.72939 2.37873 2.85832 0.24244 2 t x - - + 0.03610 4.03273 4.03273 1.46634 0.26236 1.09861 0.40547 + 2 2.84764 2.33775 2.99223 0.22904 2 t x - - 1.38629 1.38629 1.38629 1.38629 - 0.03725 4.00179 4.00179 1.46634 0.26236 1.09861 0.40547 - 3 0.16099 3.16370 2.87328 2.99734 3 a x - - + 0.03318 4.11545 4.11545 1.46634 0.26236 1.09861 0.40547 + 3 0.23331 2.81609 2.55800 2.64795 3 a x - - 1.38629 1.38629 1.38629 1.38629 - 0.03604 4.03416 4.03416 1.46634 0.26236 1.09861 0.40547 - 4 1.98862 2.42132 0.42649 2.10770 4 g x - - + 0.03194 4.15297 4.15297 1.46634 0.26236 1.09861 0.40547 + 4 2.10142 2.78158 0.31096 2.48849 4 g x - - 1.38629 1.38629 1.38629 1.38629 - 0.03539 4.05203 4.05203 1.46634 0.26236 1.09861 0.40547 - 5 1.96369 2.69532 0.36534 2.32099 5 g x - - + 0.03116 4.17730 4.17730 1.46634 0.26236 1.09861 0.40547 + 5 2.03766 2.72525 0.33174 2.44801 5 g x - - 1.38629 1.38629 1.38629 1.38629 - 0.03764 4.06427 3.92372 1.46634 0.26236 1.09861 0.40547 - 6 2.56994 2.11239 2.71946 0.30571 6 t x - - - 1.37159 1.41129 1.39124 1.37159 - 0.03806 3.89715 4.07214 1.48830 0.25587 1.07889 0.41548 - 7 2.58388 2.10353 2.64646 0.31253 12 t x - - - 1.38764 1.38524 1.38764 1.38465 - 0.03494 4.03864 4.09125 1.43264 0.27270 1.09736 0.40609 - 8 2.18552 2.70201 0.28821 2.64645 14 g x - - + 0.03089 4.19229 4.17979 1.46634 0.26236 1.09861 0.40547 + 6 2.50266 2.06695 2.58843 0.33348 6 t x - - + 1.38538 1.38782 1.38660 1.38538 + 0.03244 4.19073 4.08723 1.46789 0.26190 1.09694 0.40630 + 7 2.60375 2.25725 2.67883 0.28406 12 t x - - + 1.38907 1.38673 1.38907 1.38033 + 0.03193 4.10189 4.20735 1.39886 0.28353 1.08252 0.41361 + 8 2.19186 2.93555 0.26232 2.71924 14 g x - - 1.38629 1.38629 1.38629 1.38629 - 0.03628 4.09157 3.96779 1.46634 0.26236 1.09861 0.40547 - 9 2.16916 2.82142 0.28427 2.60854 15 g x - - - 1.38091 1.39033 1.38365 1.39033 - 0.03566 4.00237 4.08886 1.42105 0.27636 1.08174 0.41401 - 10 2.45517 2.15232 2.42886 0.34277 18 t x - - - 1.39065 1.39065 1.39065 1.37335 - 0.03536 4.01212 4.09576 1.42916 0.27379 1.09844 0.40555 - 11 2.10260 2.95484 0.28160 2.64222 21 g x - - - 1.36740 1.40555 1.40555 1.36740 - 0.03843 3.92069 4.02468 1.45555 0.26562 1.09860 0.40547 - 12 2.54740 0.30185 2.61355 2.21647 26 c x - - - 1.38748 1.38276 1.38748 1.38748 - 0.03457 4.05446 4.09623 1.43672 0.27142 1.08954 0.41003 - 13 0.28443 2.72003 2.32214 2.48149 28 a x - - - 1.38740 1.38740 1.38298 1.38740 - 0.03441 4.05976 4.10001 1.43856 0.27085 1.09845 0.40555 - 14 0.29412 2.55413 2.49679 2.35701 30 a x - - - 1.38194 1.39067 1.38194 1.39067 - 0.03505 4.02482 4.10005 1.42899 0.27385 1.09875 0.40540 - 15 0.18837 2.99710 2.82270 2.77556 33 a x - - - 1.39015 1.39472 1.37503 1.38539 - 0.03725 3.97815 4.02618 1.41936 0.27690 1.09910 0.40522 - 16 0.50816 2.05151 2.22111 1.82407 37 a x - - - 1.36727 1.38730 1.39683 1.39405 - 0.04830 3.89881 3.61610 1.36783 0.29391 1.08909 0.41026 - 17 2.11260 2.73141 0.29747 2.64152 41 g x - - - 1.36913 1.40376 1.40376 1.36913 - 0.03705 3.93681 4.08299 1.45644 0.26535 1.09300 0.40828 - 18 2.24459 1.90539 2.34054 0.43234 46 t x - - - 1.33632 1.42493 1.39937 1.38665 - 0.04427 3.64574 4.06297 1.63077 0.21788 1.12291 0.39354 - 19 0.44322 2.17202 2.18055 2.03175 57 a x - - - 1.41047 1.41471 1.36338 1.35797 - 0.03970 3.81957 4.07540 1.58572 0.22916 1.12604 0.39203 - 20 0.33340 2.42691 2.40824 2.25160 66 a x - - - 1.29389 1.44615 1.37917 1.43324 - 0.04223 3.70146 4.09459 1.52224 0.24619 1.08955 0.41003 - 21 2.50563 1.98543 2.69600 0.33746 74 t x - - - 1.39462 1.39462 1.42862 1.32990 - 0.04184 3.80216 3.98177 1.68754 0.20454 1.07729 0.41630 - 22 2.54484 1.97505 2.66483 0.33806 84 t x - - - 1.39134 1.39489 1.38662 1.37246 - 0.03877 3.97504 3.95038 1.41745 0.27751 1.10706 0.40127 - 23 2.10159 2.83856 0.29282 2.61635 88 g x - - - 1.39682 1.39682 1.35536 1.39682 - 0.05046 3.75402 3.65808 1.24245 0.34063 1.10542 0.40208 - 24 2.25298 0.61854 2.50691 1.29221 90 c x - - - 1.35803 1.49605 1.46737 1.24379 - 0.06091 3.28322 3.83564 1.80825 0.17906 1.14129 0.38479 - 25 1.27819 2.23285 0.76242 1.91259 106 g x - - - 1.29024 1.67349 1.68279 1.04597 - 0.05752 3.44263 3.73311 2.37512 0.09762 1.13899 0.38587 - 26 1.86925 2.58352 0.39466 2.33986 131 g x - - - 1.31084 1.49412 1.46666 1.29002 - 0.04698 3.54257 4.07715 2.06694 0.13533 1.02968 0.44180 - 27 2.38297 1.93394 2.39162 0.39800 151 t x - - - 1.33582 1.47359 1.44163 1.30411 - 0.04951 3.48445 4.03783 2.00196 0.14511 1.12431 0.39286 - 28 2.41717 2.17810 2.62774 0.32113 170 t x - - - 1.36805 1.48060 1.37439 1.32840 - 0.04849 3.50958 4.05014 2.35966 0.09922 1.12592 0.39208 - 29 2.57764 2.35132 2.56552 0.28512 194 t x - - - 1.43829 1.43458 1.24787 1.43829 - 0.04667 3.56670 4.05428 2.27140 0.10889 1.12876 0.39073 - 30 2.47248 2.07688 2.62257 0.33172 215 t x - - - 1.25120 1.52623 1.70635 1.15531 - 0.08932 3.31524 3.01336 2.61336 0.07611 1.12714 0.39150 - 31 2.25937 2.13157 2.02027 0.43957 248 t x - - - 1.18172 1.43522 1.72841 1.28150 - 0.07936 2.93117 3.77395 2.34189 0.10109 0.91545 0.51138 - 32 2.04508 2.84981 0.30490 2.58263 280 g x - - - 1.17665 1.66785 1.66218 1.16056 - 0.05998 3.23615 3.96853 2.64545 0.07362 1.07884 0.41550 - 33 2.45103 0.38098 2.56776 1.87147 317 c x - - - 1.24153 1.52524 1.60663 1.22783 - 0.05538 3.39046 3.90294 2.52486 0.08346 1.11838 0.39573 - 34 2.22082 0.36258 2.75077 2.02704 347 c x - - - 1.15008 1.62014 1.86511 1.10673 - 0.06086 3.18178 4.04341 2.75736 0.06556 1.13451 0.38799 - 35 0.27033 2.66664 2.52541 2.43767 388 a x - - - 1.24951 1.47565 1.41392 1.42074 - 0.07123 3.00373 3.95552 2.97118 0.05260 1.13905 0.38584 - 36 2.83107 2.41670 2.97197 0.22235 439 t x - - - 1.37071 1.57683 1.38637 1.23972 - 0.05293 3.45216 3.91807 2.33621 0.10169 1.11003 0.39980 - 37 2.52322 2.25084 2.45909 0.31611 465 t x - - - 1.26335 1.55077 1.59008 1.19965 - 0.07504 3.13329 3.55006 2.90286 0.05643 1.10636 0.40161 - 38 0.45807 2.30687 1.98940 2.03143 512 a x - - - 1.15472 1.67511 1.53797 1.26320 - 0.09820 3.13076 2.99876 2.62156 0.07547 1.16981 0.37168 - 39 2.37471 0.42180 2.44763 1.80427 550 c x - - - 1.23785 1.49058 1.48364 1.35502 - 0.06081 3.19472 4.01643 2.26388 0.10975 1.04403 0.43391 - 40 2.32826 1.95481 2.36781 0.40458 578 t x - - - 1.36586 1.46001 1.43000 1.29720 - 0.05257 3.39673 4.03256 1.75730 0.18936 1.17882 0.36765 - 41 2.68669 2.13935 2.81520 0.28200 592 t x - - - 1.34965 1.42793 1.45781 1.31633 - 0.04735 3.57826 3.99988 1.93109 0.15664 1.13176 0.38929 - 42 2.55904 2.16444 2.70859 0.29952 609 t x - - - 1.12072 1.61936 1.63578 1.26895 - 0.07346 3.25910 3.42962 2.65714 0.07273 1.16768 0.37264 - 43 1.99923 1.61027 2.26343 0.57851 646 t x - - - 1.32290 1.58747 1.61095 1.11018 - 0.06656 3.08568 3.97944 2.30872 0.10468 0.98144 0.46964 - 44 0.23887 2.79899 2.55209 2.60783 675 a x - - - 1.18557 1.50323 1.59070 1.31590 - 0.05597 3.38637 3.88222 2.28298 0.10756 1.13989 0.38545 - 45 0.29593 2.53488 2.53903 2.32335 701 a x - - - 1.08710 1.54222 1.59276 1.40430 - 0.07539 2.94521 3.91062 1.84934 0.17119 1.12860 0.39080 - 46 2.58352 2.40524 2.76700 0.25955 725 t x - - - 1.19685 1.58503 1.74852 1.14293 - 0.06124 3.18279 4.02089 2.64816 0.07341 1.08734 0.41115 - 47 2.13251 2.88788 0.29508 2.50964 764 g x - - - 1.20891 1.55463 1.68206 1.19000 - 0.06526 3.12574 3.94910 2.27651 0.10830 1.09988 0.40483 - 48 2.23841 2.99164 0.25118 2.72900 792 g x - - - 1.26330 1.55339 1.52606 1.24355 - 0.05464 3.34968 4.01313 2.57858 0.07891 1.11066 0.39949 - 49 2.57533 0.32900 2.64632 2.01501 824 c x - - - 1.35118 1.39828 1.40141 1.39516 - 0.04340 3.79297 3.91506 1.54788 0.23914 1.12122 0.39435 - 50 0.46433 2.04127 2.23437 2.00605 833 a x - - - 1.23062 1.36903 1.62282 1.36182 - 0.05764 3.31530 3.92762 2.13660 0.12563 1.09396 0.40780 - 51 0.27513 2.77017 2.28518 2.57549 853 a x - - - 1.27958 1.58726 1.46109 1.25394 - 0.05750 3.30072 3.96214 2.42368 0.09277 1.13333 0.38855 - 52 0.20149 2.86434 2.84551 2.69770 883 a x - - - 1.23645 1.62259 1.71174 1.10368 - 0.05756 3.26729 4.02702 2.37267 0.09787 1.13770 0.38648 - 53 0.26982 2.65833 2.50477 2.46835 911 a x - - - 1.36005 1.50358 1.48100 1.22550 - 0.06921 3.37553 3.42118 2.19529 0.11802 1.13826 0.38622 - 54 0.40022 2.19284 2.22687 2.20396 934 a x - - - 1.12070 1.60472 1.53213 1.35895 - 0.05523 3.36752 3.94966 2.24890 0.11151 1.02145 0.44640 - 55 2.11356 0.46400 2.46442 1.79955 960 c x - - - 1.23932 1.35913 1.50478 1.46331 - 0.05187 3.47055 3.94022 2.17140 0.12106 1.10399 0.40279 - 56 1.85868 0.79440 2.22069 1.25971 983 c x - - - 1.21951 1.50212 1.51138 1.34185 - 0.06404 3.29054 3.69705 1.69351 0.20318 1.11833 0.39575 - 57 1.33272 2.32720 0.71452 1.90215 999 g x - - - 1.12229 1.49343 1.56653 1.42255 - 0.04920 3.46654 4.08749 2.02027 0.14228 1.15003 0.38072 - 58 2.48337 0.43652 2.46331 1.68683 1017 c x - - - 1.34704 1.55461 1.38112 1.28222 - 0.04823 3.61532 3.90311 2.01908 0.14246 1.07530 0.41733 - 59 0.41659 2.44509 1.93972 2.20507 1034 a x - - - 1.38198 1.38198 1.39194 1.38932 - 0.03641 3.98130 4.06929 1.40885 0.28028 1.14581 0.38268 - 60 0.41612 2.39160 1.97116 2.21075 1037 a x - - - 1.03649 1.46430 1.57421 1.57557 - 0.04769 3.52580 4.06641 2.13225 0.12621 1.03124 0.44093 - 61 2.66264 2.12302 2.82746 0.28581 1056 t x - - - 1.36925 1.39635 1.38930 1.39048 - 0.04097 3.97400 3.84718 1.42709 0.27444 1.10349 0.40304 - 62 2.26510 2.13196 2.42551 0.37231 1060 t x - - - 1.37965 1.39147 1.39147 1.38264 - 0.04082 3.91610 3.90805 1.34598 0.30149 1.06394 0.42326 - 63 0.41244 2.25761 2.16787 2.12907 1062 a x - - - 1.34515 1.41203 1.41203 1.37753 - 0.04054 3.77835 4.08203 1.36896 0.29353 1.10284 0.40336 - 64 2.51464 0.37905 2.62296 1.82008 1068 c x - - - 1.39543 1.38753 1.39233 1.37008 - 0.03854 3.90584 4.03535 1.40940 0.28010 1.10667 0.40146 - 65 2.16380 2.11332 2.18714 0.42765 1073 t x - - - 1.38764 1.38471 1.38519 1.38764 - 0.03575 4.05376 4.03073 1.43270 0.27268 1.08530 0.41219 - 66 2.79349 2.39141 2.87271 0.23478 1075 t x - - - 1.37227 1.39101 1.39101 1.39101 - 0.03597 4.01447 4.05827 1.42619 0.27473 1.09128 0.40915 - 67 2.82488 2.47749 2.93179 0.21887 1078 t x - - - 1.38141 1.39112 1.38915 1.38353 - 0.03661 3.99477 4.04370 1.40962 0.28003 1.10594 0.40182 - 68 2.77679 2.30433 2.90694 0.24425 1081 t x - - - 1.37593 1.38989 1.45520 1.32825 - 0.04447 3.68736 3.99242 1.66809 0.20900 1.07378 0.41811 - 69 2.47698 3.17398 0.19595 2.95437 1093 g x - - - 1.38264 1.38264 1.39734 1.38264 - 0.05358 3.96553 3.40487 1.43194 0.27292 1.08430 0.41270 - 70 2.84327 0.27906 2.97336 2.00890 1097 c x - - + 0.03142 4.21107 4.12859 1.46634 0.26236 1.09861 0.40547 + 9 2.07901 2.78051 0.30613 2.56850 15 g x - - + 1.38350 1.38805 1.38560 1.38805 + 0.03149 4.16813 4.16598 1.44243 0.26965 1.09240 0.40859 + 10 2.57980 2.23058 2.70339 0.28799 18 t x - - + 1.38730 1.38730 1.38730 1.38328 + 0.03029 4.19523 4.21518 1.45741 0.26506 1.09679 0.40638 + 11 2.09819 2.95912 0.27277 2.74586 21 g x - - + 1.38506 1.38753 1.38753 1.38506 + 0.03438 4.20499 3.96976 1.46555 0.26260 1.09847 0.40554 + 12 2.73996 0.25202 2.91136 2.26531 26 c x - - + 1.38701 1.38416 1.38701 1.38701 + 0.03125 4.18883 4.16044 1.44829 0.26784 1.07539 0.41728 + 13 0.27970 2.57147 2.50665 2.45312 28 a x - - + 1.38695 1.38695 1.38433 1.38695 + 0.03063 4.20139 4.18737 1.44978 0.26739 1.09652 0.40651 + 14 0.27532 2.53583 2.54819 2.48584 30 a x - - + 1.38514 1.38745 1.38514 1.38745 + 0.03161 4.20713 4.12095 1.45611 0.26545 1.10038 0.40458 + 15 0.22434 2.72071 2.78113 2.61512 33 a x - - + 1.38788 1.38927 1.38318 1.38486 + 0.03686 4.17327 3.87329 1.44180 0.26984 1.10484 0.40236 + 16 0.43251 2.24579 2.21906 1.99092 37 a x - - + 1.36200 1.39388 1.39592 1.39378 + 0.04715 3.92767 3.63579 1.28473 0.32397 1.06747 0.42141 + 17 2.14020 2.88555 0.27611 2.69098 41 g x - - + 1.38394 1.38865 1.38865 1.38394 + 0.03184 4.19737 4.11610 1.46485 0.26281 1.06375 0.42336 + 18 2.54908 2.09631 2.66371 0.31574 46 t x - - + 1.38086 1.39134 1.39054 1.38248 + 0.03937 4.05640 3.84942 1.45345 0.26626 1.11413 0.39779 + 19 0.45711 2.16557 2.17736 1.97423 57 a x - - + 1.38787 1.39103 1.38646 1.37985 + 0.03547 4.14271 3.96510 1.44704 0.26823 1.13642 0.38708 + 20 0.30358 2.53734 2.46922 2.32172 66 a x - - + 1.37069 1.39228 1.38994 1.39244 + 0.03311 4.09596 4.13961 1.41439 0.27849 1.11423 0.39775 + 21 2.54370 2.06068 2.71024 0.31809 74 t x - - + 1.38671 1.38671 1.38837 1.38339 + 0.04565 4.21460 3.51159 1.48099 0.25801 1.14016 0.38532 + 22 2.44416 2.09512 2.52049 0.34288 84 t x - - + 1.38754 1.39327 1.39136 1.37313 + 0.04852 4.04797 3.50981 1.37593 0.29116 1.16476 0.37396 + 23 2.14524 2.93015 0.27618 2.64656 88 g x - 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