1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
|
\expandafter\ifx\csname graph\endcsname\relax \csname newbox\endcsname\graph\fi
\expandafter\ifx\csname graphtemp\endcsname\relax \csname newdimen\endcsname\graphtemp\fi
\setbox\graph=\vtop{\vskip 0pt\hbox{%
\special{pn 8}%
\special{ar 2618 294 706 294 0 6.28319}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 0.294in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss option\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 0.294in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss parsing\hss}}%
\special{pa 1912 1676}%
\special{pa 3324 1676}%
\special{pa 3324 1088}%
\special{pa 1912 1088}%
\special{pa 1912 1676}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 1.382in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss all options\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 1.382in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss passed to program\hss}}%
\special{ar 2618 2471 706 294 0 6.28319}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 2.471in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss loading\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 2.471in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss input files\hss}}%
\special{pa 1912 4206}%
\special{pa 3324 4206}%
\special{pa 3324 3265}%
\special{pa 1912 3265}%
\special{pa 1912 4206}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -3\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 3.735in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss input files:\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 3.735in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss genomic sequence\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 3.735in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss reference sequence\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 3\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 3.735in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss splice site param.\hss}}%
\special{ar 2618 5000 706 294 0 6.28319}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 5.000in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss similarity\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 5.000in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss filter\hss}}%
\special{pa 1912 6382}%
\special{pa 3324 6382}%
\special{pa 3324 5794}%
\special{pa 1912 5794}%
\special{pa 1912 6382}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 6.088in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss List of\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 6.088in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss Hits\hss}}%
\special{pa 0 6382}%
\special{pa 1412 6382}%
\special{pa 1412 5794}%
\special{pa 0 5794}%
\special{pa 0 6382}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 6.088in
\rlap{\kern 0.706in\lower\graphtemp\hbox to 0pt{\hss DP\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 6.088in
\rlap{\kern 0.706in\lower\graphtemp\hbox to 0pt{\hss parameter\hss}}%
\special{ar 2618 7529 1059 441 0 6.28319}%
\graphtemp=\baselineskip\multiply\graphtemp by -2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 7.529in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss DP algorithm\hss}}%
\graphtemp=.5ex\advance\graphtemp by 7.529in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss for optimal\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 7.529in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss spliced alignment\hss}}%
\special{pa 4176 7824}%
\special{pa 5588 7824}%
\special{pa 5588 7235}%
\special{pa 4176 7235}%
\special{pa 4176 7824}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 7.529in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss one spliced\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 7.529in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss alignment\hss}}%
\special{ar 4882 6294 1059 441 0 6.28319}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 6.294in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss spliced alignment\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 6.294in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss collection\hss}}%
\special{pa 4176 5353}%
\special{pa 5588 5353}%
\special{pa 5588 4765}%
\special{pa 4176 4765}%
\special{pa 4176 5353}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 5.059in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss binary search tree\hss}}%
\graphtemp=.5ex\advance\graphtemp by 5.059in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss of spliced\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 5.059in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss alignments\hss}}%
\special{ar 4882 3971 706 294 0 6.28319}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 3.971in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss output spliced\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 3.971in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss alignments\hss}}%
\special{pa 4176 3176}%
\special{pa 5588 3176}%
\special{pa 5588 2588}%
\special{pa 4176 2588}%
\special{pa 4176 3176}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 2.882in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss output\hss}}%
\graphtemp=.5ex\advance\graphtemp by 2.882in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss of spliced\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 2.882in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss alignments\hss}}%
\special{pa 3824 1676}%
\special{pa 5235 1676}%
\special{pa 5235 1088}%
\special{pa 3824 1088}%
\special{pa 3824 1676}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 1.382in
\rlap{\kern 4.529in\lower\graphtemp\hbox to 0pt{\hss BSSM\hss}}%
\graphtemp=.5ex\advance\graphtemp by 1.382in
\rlap{\kern 4.529in\lower\graphtemp\hbox to 0pt{\hss parameter\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 1.382in
\rlap{\kern 4.529in\lower\graphtemp\hbox to 0pt{\hss files\hss}}%
\special{ar 6441 1382 706 294 0 6.28319}%
\graphtemp=.5ex\advance\graphtemp by 1.382in
\rlap{\kern 6.441in\lower\graphtemp\hbox to 0pt{\hss mkbssmfiles.x\hss}}%
\special{pa 0 2765}%
\special{pa 1412 2765}%
\special{pa 1412 2176}%
\special{pa 0 2176}%
\special{pa 0 2765}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 2.471in
\rlap{\kern 0.706in\lower\graphtemp\hbox to 0pt{\hss index of\hss}}%
\graphtemp=.5ex\advance\graphtemp by 2.471in
\rlap{\kern 0.706in\lower\graphtemp\hbox to 0pt{\hss genomic and\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 2\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 2.471in
\rlap{\kern 0.706in\lower\graphtemp\hbox to 0pt{\hss reference sequence\hss}}%
\special{ar 706 1382 706 294 0 6.28319}%
\graphtemp=.5ex\advance\graphtemp by 1.382in
\rlap{\kern 0.706in\lower\graphtemp\hbox to 0pt{\hss mkvtree.x\hss}}%
\special{pa 2618 588}%
\special{pa 2618 1088}%
\special{fp}%
\special{sh 1.000}%
\special{pa 2643 988}%
\special{pa 2618 1088}%
\special{pa 2593 988}%
\special{pa 2643 988}%
\special{fp}%
\special{pa 2618 1676}%
\special{pa 2618 2176}%
\special{fp}%
\special{sh 1.000}%
\special{pa 2643 2076}%
\special{pa 2618 2176}%
\special{pa 2593 2076}%
\special{pa 2643 2076}%
\special{fp}%
\special{pa 2618 2765}%
\special{pa 2618 3265}%
\special{fp}%
\special{sh 1.000}%
\special{pa 2643 3165}%
\special{pa 2618 3265}%
\special{pa 2593 3165}%
\special{pa 2643 3165}%
\special{fp}%
\special{pa 2618 4206}%
\special{pa 2618 4706}%
\special{fp}%
\special{sh 1.000}%
\special{pa 2643 4606}%
\special{pa 2618 4706}%
\special{pa 2593 4606}%
\special{pa 2643 4606}%
\special{fp}%
\special{pa 2618 5294}%
\special{pa 2618 5794}%
\special{fp}%
\special{sh 1.000}%
\special{pa 2643 5694}%
\special{pa 2618 5794}%
\special{pa 2593 5694}%
\special{pa 2643 5694}%
\special{fp}%
\special{pa 2618 5294}%
\special{pa 706 5794}%
\special{fp}%
\special{sh 1.000}%
\special{pa 809 5793}%
\special{pa 706 5794}%
\special{pa 796 5745}%
\special{pa 809 5793}%
\special{fp}%
\special{pa 706 6382}%
\special{pa 2618 7088}%
\special{fp}%
\special{sh 1.000}%
\special{pa 2532 7030}%
\special{pa 2618 7088}%
\special{pa 2515 7077}%
\special{pa 2532 7030}%
\special{fp}%
\special{pa 2618 6382}%
\special{pa 2618 7088}%
\special{fp}%
\special{sh 1.000}%
\special{pa 2643 6988}%
\special{pa 2618 7088}%
\special{pa 2593 6988}%
\special{pa 2643 6988}%
\special{fp}%
\graphtemp=\baselineskip\multiply\graphtemp by -1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 6.735in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss for every\hss}}%
\graphtemp=\baselineskip\multiply\graphtemp by 1\divide\graphtemp by 2
\advance\graphtemp by .5ex\advance\graphtemp by 6.735in
\rlap{\kern 2.618in\lower\graphtemp\hbox to 0pt{\hss hit\hss}}%
\special{pa 3676 7529}%
\special{pa 4176 7529}%
\special{fp}%
\special{sh 1.000}%
\special{pa 4076 7504}%
\special{pa 4176 7529}%
\special{pa 4076 7554}%
\special{pa 4076 7504}%
\special{fp}%
\special{pa 4882 7235}%
\special{pa 4882 6735}%
\special{da 0.050}%
\special{sh 1.000}%
\special{pa 4857 6835}%
\special{pa 4882 6735}%
\special{pa 4907 6835}%
\special{pa 4857 6835}%
\special{fp}%
\graphtemp=.5ex\advance\graphtemp by 6.985in
\rlap{\kern 4.882in\lower\graphtemp\hbox to 0pt{\hss possibly\hss}}%
\special{pa 4882 5853}%
\special{pa 4882 5353}%
\special{fp}%
\special{sh 1.000}%
\special{pa 4857 5453}%
\special{pa 4882 5353}%
\special{pa 4907 5453}%
\special{pa 4857 5453}%
\special{fp}%
\special{pa 4882 4765}%
\special{pa 4882 4265}%
\special{fp}%
\special{sh 1.000}%
\special{pa 4857 4365}%
\special{pa 4882 4265}%
\special{pa 4907 4365}%
\special{pa 4857 4365}%
\special{fp}%
\special{pa 4882 3676}%
\special{pa 4882 3176}%
\special{fp}%
\special{sh 1.000}%
\special{pa 4857 3276}%
\special{pa 4882 3176}%
\special{pa 4907 3276}%
\special{pa 4857 3276}%
\special{fp}%
\special{pa 4529 1676}%
\special{pa 3324 2471}%
\special{fp}%
\special{sh 1.000}%
\special{pa 3421 2436}%
\special{pa 3324 2471}%
\special{pa 3393 2395}%
\special{pa 3421 2436}%
\special{fp}%
\special{pa 5735 1382}%
\special{pa 5235 1382}%
\special{fp}%
\special{sh 1.000}%
\special{pa 5335 1407}%
\special{pa 5235 1382}%
\special{pa 5335 1357}%
\special{pa 5335 1407}%
\special{fp}%
\special{pa 1412 2471}%
\special{pa 1912 2471}%
\special{fp}%
\special{sh 1.000}%
\special{pa 1812 2446}%
\special{pa 1912 2471}%
\special{pa 1812 2496}%
\special{pa 1812 2446}%
\special{fp}%
\special{pa 706 1676}%
\special{pa 706 2176}%
\special{fp}%
\special{sh 1.000}%
\special{pa 731 2076}%
\special{pa 706 2176}%
\special{pa 681 2076}%
\special{pa 731 2076}%
\special{fp}%
\hbox{\vrule depth7.971in width0pt height 0pt}%
\kern 7.147in
}%
}%
|
