New upstream version 2.0.0 (b12160d8) · Commits · Debian Med / trnascan-se

Archaea-BHB-noncan.cm

deleted100644 → 0

+0 −167

Original line number	Diff line number	Diff line
		INFERNAL-1 [1.0]
		NAME Archaea-NC-Intron
		STATES 124
		NODES 28
		ALPHABET 1
		ELSELF -0.08926734
		WBETA 1e-07
		NSEQ 148
		EFFNSEQ 148.000
		CLEN 40
		BCOM cmbuild --rf --enone -F Archaea-BHB-noncan.cm Archaea-BHB-noncan.sto
		BDATE Wed Aug 5 18:38:10 2009
		NULL 0.000 0.000 0.000 0.000
		MODEL:
		[ ROOT 0 ]
		S 0 -1 0 1 6 -13.180 -13.120 -0.001 -11.896 -12.176 -12.571
		IL 1 1 2 1 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 2 2 3 2 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 1 ]
		MP 3 2 3 7 6 -13.180 -13.120 -0.001 -11.896 -12.176 -12.571 -0.553 0.180 -0.805 -1.580 0.039 -0.132 1.032 -0.961 1.087 0.350 -0.302 -3.122 -0.376 0.222 0.847 -0.473
		ML 4 2 3 7 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 5 2 3 7 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076
		D 6 2 3 7 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
		IL 7 7 5 7 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 8 8 6 8 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 2 ]
		MP 9 8 6 13 6 -13.180 -13.120 -0.001 -11.896 -12.176 -12.571 -0.679 0.345 -1.278 0.217 -1.335 0.610 0.158 -2.094 -0.942 1.328 0.852 -0.808 -0.468 0.384 0.241 -0.638
		ML 10 8 6 13 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 11 8 6 13 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076
		D 12 8 6 13 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
		IL 13 13 5 13 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 14 14 6 14 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 3 ]
		MP 15 14 6 19 6 -13.180 -13.120 -0.001 -11.896 -12.176 -12.571 -3.085 -0.094 0.388 0.575 -4.100 -1.284 0.323 -0.315 0.485 1.652 0.861 0.534 -1.310 -0.940 -0.533 -2.306
		ML 16 14 6 19 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 17 14 6 19 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076
		D 18 14 6 19 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
		IL 19 19 5 19 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 20 20 6 20 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 4 ]
		MP 21 20 6 25 6 -13.180 -13.120 -0.001 -11.896 -12.176 -12.571 -1.627 1.032 0.144 0.574 -0.502 0.326 0.474 -1.619 -0.731 1.846 -0.268 -0.507 -2.731 -2.115 0.115 -2.573
		ML 22 20 6 25 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 23 20 6 25 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076
		D 24 20 6 25 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
		IL 25 25 5 25 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 26 26 6 26 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 5 ]
		MP 27 26 6 31 4 -12.154 -6.639 -0.016 -9.853 -4.149 -2.051 0.059 -2.692 -0.481 -0.348 1.371 -0.318 -1.425 2.266 -0.515 0.197 -1.021 -0.781 -0.408 -0.402
		ML 28 26 6 31 4 -2.408 -4.532 -1.293 -1.473 0.660 -0.612 -0.293 -0.076
		MR 29 26 6 31 4 -4.102 -12.528 -0.390 -2.485 0.660 -0.612 -0.293 -0.076
		D 30 26 6 31 4 -12.737 -14.007 -2.036 -0.404
		IL 31 31 5 31 4 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000
		IR 32 32 6 32 3 -3.062 -0.226 -5.301 0.000 0.000 0.000 0.000
		[ MATR 6 ]
		MR 33 32 6 35 3 -13.564 -0.001 -11.882 -0.041 -0.728 0.409 0.133
		D 34 32 6 35 3 -6.390 -1.568 -0.620
		IR 35 35 3 35 3 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
		[ MATR 7 ]
		MR 36 35 3 38 3 -13.564 -0.001 -11.882 0.773 -1.034 0.652 -2.111
		D 37 35 3 38 3 -6.390 -1.568 -0.620
		IR 38 38 3 38 3 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
		[ MATR 8 ]
		MR 39 38 3 41 5 -12.207 -0.001 -12.022 -12.234 -13.126 1.907 -3.509 -3.041 -4.637
		D 40 38 3 41 5 -5.352 -0.707 -2.978 -4.409 -2.404
		IR 41 41 3 41 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 9 ]
		MP 42 41 3 46 6 -13.180 -13.120 -0.001 -11.896 -12.176 -12.571 -4.303 -2.311 -0.025 -0.706 -4.219 -1.631 2.474 -4.243 -2.815 1.438 -4.589 1.376 0.264 -1.749 0.162 -4.067
		ML 43 41 3 46 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 44 41 3 46 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076
		D 45 41 3 46 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
		IL 46 46 5 46 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 47 47 6 47 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 10 ]
		MP 48 47 6 52 6 -13.180 -13.120 -0.001 -11.896 -12.176 -12.571 -6.894 -3.183 -7.771 0.944 -8.050 -7.689 2.211 -7.339 -7.035 2.653 -2.529 -1.595 0.838 -7.036 -0.516 -6.190
		ML 49 47 6 52 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 50 47 6 52 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076
		D 51 47 6 52 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
		IL 52 52 5 52 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 53 53 6 53 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 11 ]
		MP 54 53 6 58 6 -13.180 -13.120 -0.001 -11.896 -12.176 -12.571 -7.157 -6.147 -8.101 0.723 -8.763 -7.957 1.793 -7.599 -7.277 3.124 -6.961 -0.665 -0.023 -7.318 -1.411 -3.113
		ML 55 53 6 58 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 56 53 6 58 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076
		D 57 53 6 58 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
		IL 58 58 5 58 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 59 59 6 59 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 12 ]
		MP 60 59 6 64 4 -12.357 -12.564 -0.001 -10.978 -6.403 -7.081 -0.862 -0.921 -6.146 -2.492 2.202 -7.461 -1.224 2.604 -7.540 -5.329 -1.275 -6.909 1.647 -6.316
		ML 61 59 6 64 4 -3.758 -3.940 -0.507 -2.670 0.660 -0.612 -0.293 -0.076
		MR 62 59 6 64 4 -4.809 -3.838 -1.706 -0.766 0.660 -0.612 -0.293 -0.076
		D 63 59 6 64 4 -4.568 -4.250 -2.265 -0.520
		IL 64 64 5 64 4 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
		IR 65 65 6 65 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
		[ MATL 13 ]
		ML 66 65 6 68 3 -13.269 -0.001 -11.923 0.690 -0.282 0.156 -1.154
		D 67 65 6 68 3 -6.174 -1.687 -0.566
		IL 68 68 3 68 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
		[ MATL 14 ]
		ML 69 68 3 71 3 -13.269 -0.001 -11.923 -0.439 0.123 0.805 -1.229
		D 70 68 3 71 3 -6.174 -1.687 -0.566
		IL 71 71 3 71 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
		[ MATL 15 ]
		ML 72 71 3 74 5 -12.207 -0.047 -6.886 -7.136 -5.962 1.545 -2.377 -1.607 -0.833
		D 73 71 3 74 5 -4.959 -0.803 -4.221 -2.596 -2.508
		IL 74 74 3 74 5 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
		[ MATP 16 ]
		MP 75 74 3 79 6 -13.136 -13.076 -0.060 -11.852 -5.374 -5.957 -11.758 -10.096 -11.268 -2.214 -8.937 -12.516 2.537 -10.139 -12.707 2.974 -11.780 -1.382 0.621 -12.752 -2.356 -8.766
		ML 76 74 3 79 6 -7.725 -8.071 -2.786 -2.480 -7.921 -0.592 1.593 -1.856 -1.723 -1.306
		MR 77 74 3 79 6 -8.189 -6.918 -2.827 -6.897 -0.304 -5.110 1.532 -1.693 -1.530 -1.142
		D 78 74 3 79 6 -11.481 -10.179 -5.976 -6.659 -6.676 -0.054
		IL 79 79 5 79 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 80 80 6 80 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 17 ]
		MP 81 80 6 85 6 -13.078 -13.017 -0.176 -11.793 -5.650 -3.410 -6.750 -5.892 -2.749 0.736 -1.367 -7.583 1.586 -7.223 -3.149 3.082 -6.660 -1.920 0.457 -6.909 -0.988 -6.076
		ML 82 80 6 85 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 83 80 6 85 6 -9.755 -8.484 -0.495 -8.462 -1.869 -6.675 -0.920 -1.582 0.789 0.496
		D 84 80 6 85 6 -12.642 -11.340 -7.137 -7.819 -7.837 -0.024
		IL 85 85 5 85 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 86 86 6 86 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 18 ]
		MP 87 86 6 91 6 -12.944 -12.883 -0.328 -11.659 -6.872 -2.366 -3.574 -3.158 -2.975 1.051 -7.669 -7.356 2.093 -2.601 -2.084 2.718 -6.456 -0.740 0.602 -6.710 -2.354 -5.916
		ML 88 86 6 91 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 89 86 6 91 6 -9.540 -8.269 -0.177 -8.247 -3.381 -6.460 0.375 0.213 -0.189 -0.586
		D 90 86 6 91 6 -14.258 -12.956 -8.753 -9.436 -9.453 -0.008
		IL 91 91 5 91 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 92 92 6 92 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 19 ]
		MP 93 92 6 97 6 -12.670 -12.610 -0.354 -11.386 -6.521 -2.281 -6.550 -2.506 -7.481 0.718 -8.079 -7.352 2.827 -2.550 -6.675 2.376 -6.366 -0.382 -0.569 -6.707 -2.291 -5.871
		ML 94 92 6 97 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
		MR 95 92 6 97 6 -8.230 -6.959 -2.868 -6.937 -0.295 -5.151 1.550 -1.738 -1.583 -1.187
		D 96 92 6 97 6 -15.439 -14.137 -9.934 -10.616 -10.634 -0.003
		IL 97 97 5 97 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
		IR 98 98 6 98 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
		[ MATP 20 ]
		MP 99 98 6 103 4 -11.450 -11.657 -0.895 -1.115 -5.905 -5.479 -2.092 0.063 -5.605 -6.755 2.924 -6.315 -2.962 2.213 -6.075 -0.726 0.130 -6.037 -0.914 -5.097
		ML 100 98 6 103 4 -3.758 -3.940 -0.507 -2.670 0.660 -0.612 -0.293 -0.076
		MR 101 98 6 103 4 -6.893 -5.922 -0.258 -2.850 0.633 -1.416 0.599 -0.836
		D 102 98 6 103 4 -11.437 -11.119 -9.134 -0.004
		IL 103 103 5 103 4 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
		IR 104 104 6 104 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
		[ MATL 21 ]
		ML 105 104 6 107 3 -11.550 -0.002 -10.204 -1.502 0.882 0.329 -0.868
		D 106 104 6 107 3 -14.171 -0.004 -8.562
		IL 107 107 3 107 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
		[ MATL 22 ]
		ML 108 107 3 110 3 -13.269 -0.011 -7.094 0.051 0.101 0.211 -0.445
		D 109 107 3 110 3 -6.174 -1.687 -0.566
		IL 110 110 3 110 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
		[ MATL 23 ]
		ML 111 110 3 113 3 -0.900 -2.036 -2.183 -0.109 0.249 0.323 -0.660
		D 112 110 3 113 3 -8.015 -0.308 -2.406
		IL 113 113 3 113 3 -0.249 -2.656 -12.425 0.000 0.000 0.000 0.000
		[ MATL 24 ]
		ML 114 113 3 116 3 -12.913 -0.001 -11.567 0.106 -0.048 -0.126 0.056
		D 115 113 3 116 3 -12.510 -0.012 -6.902
		IL 116 116 3 116 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
		[ MATL 25 ]
		ML 117 116 3 119 3 -13.269 -1.720 -0.522 0.226 -0.054 0.162 -0.417
		D 118 116 3 119 3 -6.174 -1.687 -0.566
		IL 119 119 3 119 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
		[ MATL 26 ]
		ML 120 119 3 122 2 * 0.000 -1.563 0.297 0.962 -1.042
		D 121 119 3 122 2 * 0.000
		IL 122 122 3 122 2 -1.823 -0.479 0.000 0.000 0.000 0.000
		[ END 27 ]
		E 123 122 3 -1 0
		//

COPYING

+4 −4

Original line number	Diff line number	Diff line
		tRNAscan-SE -- a program for finding transfer RNAs

		Copyright (C) 1996 Todd M.J. Lowe & Sean R. Eddy
		Copyright (C) 2017 Patricia P. Chan, Brian Lin, and Todd M. Lowe

		This set of programs is free software; you can redistribute it and/or
		modify it under the terms of the GNU General Public License as
		published by the Free Software Foundation; either version 2 of the
		published by the Free Software Foundation; either version 3 of the
		License, or (at your option) any later version.

		This program is distributed in the hope that it will be useful, but
		@@ -13,8 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
		General Public License for more details.

		You should have received a copy of the GNU General Public License
		along with this program, in the file GNULICENSE; if not, write to the Free
		Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139 USA.
		along with this program, in the file GNULICENSE; if not, check out
		the web site at https://www.gnu.org/licenses/gpl-3.0.en.html.

		This distribution includes source code originally derived from other
		sources. In particular, modified source code from the program

Cove/COPYING

deleted100644 → 0

+0 −28

Original line number	Diff line number	Diff line
		cove -- programs to apply covariance models to RNA sequence analysis

		Copyright (C) 1993,1994 Sean R. Eddy

		This set of programs is free software; you can redistribute it and/or
		modify it under the terms of the GNU General Public License as
		published by the Free Software Foundation; either version 2 of the
		License, or (at your option) any later version.

		This program is distributed in the hope that it will be useful, but
		WITHOUT ANY WARRANTY; without even the implied warranty of
		MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
		General Public License for more details.

		You should have received a copy of the GNU General Public License
		along with this program, in the file GNULICENSE; if not, write to the Free
		Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139 USA.

		This distribution may include source code originally derived from
		other sources. In particular, my general sequence library includes
		source code that derives from Henry Spencer (regexp() functions), and
		Don Gilbert (sequence i/o functions). Borrowed code is annotated and
		credited in the source files whenever it appears. The copying policies
		of my benefactors are compatible with the GNU Public License under
		which this package is distributed.

Cove/DEMO

deleted100644 → 0

+0 −105

Original line number	Diff line number	Diff line

		Demonstrations of the covariance model programs
		-----------------------------------------------

		As an introduction to how the software works, this file contains
		instructions on how to reproduce the results in our paper. (Note
		that this version of the code is newer, somewhat less buggy, and
		faster than the version used for our original experiments. There may
		be minor differences between the results we report in our paper and
		the results you get from these demos.)

		For more details, refer to S.R. Eddy and R. Durbin, "RNA Sequence
		Analysis Using Covariance Models", NAR 22:2079-2088, 1994.

		The directory Demos/ contains the data files:

		TRNA2.cm - A very good tRNA model
		7SL-euk.cm - A model of 7SL signal recognition particle RNA
		7SL-euk.fa - 37 eukaryotic 7SL RNAs (includes some fragments)
		trna1415.slx - Steinberg/Sprinzl trusted tRNA alignment
		sim65.slx - alignment of 100 dissimilar tRNAs
		sim100.slx - alignment of 100 randomly chosen tRNAs
		test100.fa - 100 unaligned, randomly chosen independent test tRNAs
		sim65.fa - unaligned SIM65 sequences
		sim100.fa - unaligned SIM100 sequences
		fig5.slx - Trusted alignment of 5 tRNAs, from our figure 5
		fig5.fa - unaligned tRNA sequences of fig5.slx
		yeast-phe.fa - S. cerevisiae tRNA-Phe sequence
		K11H3frag.fa - fragment of C. elegans cosmid K11H3, which contains 2 tRNA genes

		## Constructing a model from trusted alignments:

		> covet -a sim100.slx A100.cm sim100.fa
		> covet -a sim65.slx A65.cm sim65.fa

		Produces models A100 and A65. Uses trusted alignments (sim100.slx,
		sim65.slx) to construct the initial models; then uses sim100.fa or
		sim65.fa as training sequences.
		Takes about fifteen minutes per model on an R4000 Indigo.

		## Constructing a model from unaligned sequences:

		> covet U100.cm sim100.fa
		> covet U65.cm sim65.fa

		Produces models U100 and U65 from unaligned training sequences in sim100.fa
		and sim65.fa.
		Takes about an hour per model on an R4000 Indigo.

		## Multiple RNA sequence alignment using a trained model:

		> covea A100.cm fig5.fa
		> covea U100.cm fig5.fa

		Produces a multiple sequence alignment of the 5 sequences in fig5.fa
		and prints it to the screen. Compare to the trusted alignment
		(fig5.slx) or our preprint's Figure 5.
		Takes about ten seconds.


		## Scoring example sequences using a trained model:

		> coves A100.cm fig5.fa

		Calculates and prints alignment scores (in bits) for the 5 sequences in
		fig5.fa.
		Takes about ten seconds.

		## Structure prediction of individual sequences using a trained model:

		> coves -s A100.cm yeast-phe.fa
		> coves -m A100.cm yeast-phe.fa

		Aligns the model A100.cm to yeast tRNA-Phe, and prints out the alignment
		score. The -s option to coves prints out a secondary structure representation
		for the sequence as well. This representation uses ">" and "<" characters
		to represent pairwise assignments. The -m option to coves produces a
		"mountain" representation of the structure. Both of these representations
		are described in a paper by Danielle Konings (Konings and Hogeweg,
		J. Mol. Biol. 207:597-614, 1989). Covariance models typically
		overpredict pairs; the predicted pairs are a superset of the
		secondary structure pairings. [One of the major weaknesses in the package at the
		moment is a lack of graphical secondary structure display and a lack of
		automatic classification of predicted pairs as secondary structure vs. tertiary
		structure or overprediction.]
		Takes about ten seconds.

		## Searching a database for new tRNAs:

		> covels -c A100.cm K11H3frag.fa

		Searches a 500 bp fragment of the C. elegans cosmid K11H3 for tRNAs,
		on both strands (the -c option asks for both strands to be searched).
		This fragment contains two predicted tRNA genes.
		Takes about two minutes.

		> covels -c -w 150 TRNA2.cm K11H3frag.fa

		Same as above, except using a model trained on 1315 different tRNA
		sequences. This model is known to recognize all known cytoplasmic
		eukaryotic tRNAs with scores > 20 bits. The -w option allows tRNAs
		up to 150 nt in length. Using covels with this model is the most
		sensitive means I know of for detecting tRNAs in genomic sequence.

Cove/Demos/7SL-euk.cm

deleted100644 → 0

+0 −4114

File deleted.

Preview size limit exceeded, changes collapsed.