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
|
\indexentry{PATH@\texttt {PATH}|hyperpage}{6}
\indexentry{BSSMDIR@\texttt {BSSMDIR}|hyperpage}{6}
\indexentry{GTHDATADIR@\texttt {GTHDATADIR}|hyperpage}{6}
\indexentry{GTHNOFLOCK@\texttt {GTHNOFLOCK}|hyperpage}{6}
\indexentry{GTHNOFLOCK@\texttt {GTHNOFLOCK}|hyperpage}{6}
\indexentry{genseqfiles\xspace @\textit {genseqfiles\xspace }|hyperpage}{6}
\indexentry{cdnafiles\xspace @\textit {cdnafiles\xspace }|hyperpage}{6}
\indexentry{proteinfiles\xspace @\textit {proteinfiles\xspace }|hyperpage}{6}
\indexentry{genseqfiles\xspace @\textit {genseqfiles\xspace }|hyperpage}{7}
\indexentry{cdnafiles\xspace @\textit {cdnafiles\xspace }|hyperpage}{7}
\indexentry{proteinfiles\xspace @\textit {proteinfiles\xspace }|hyperpage}{7}
\indexentry{error code|hyperpage}{7}
\indexentry{genseqfiles\xspace @\textit {genseqfiles\xspace }|hyperpage}{9}
\indexentry{Option!\texttt {-genomic}|hyperpage}{9}
\indexentry{genseqfiles\xspace @\textit {genseqfiles\xspace }|hyperpage}{9}
\indexentry{cdnafiles\xspace @\textit {cdnafiles\xspace }|hyperpage}{9}
\indexentry{Option!\texttt {-cdna}|hyperpage}{9}
\indexentry{cdnafiles\xspace @\textit {cdnafiles\xspace }|hyperpage}{9}
\indexentry{proteinfiles\xspace @\textit {proteinfiles\xspace }|hyperpage}{9}
\indexentry{Option!\texttt {-protein}|hyperpage}{9}
\indexentry{proteinfiles\xspace @\textit {proteinfiles\xspace }|hyperpage}{9}
\indexentry{multiple fasta|hyperpage}{9}
\indexentry{description!\Fasta|hyperpage}{9}
\indexentry{EMBL@\EMBL|hyperpage}{9}
\indexentry{SWISSPROT@\SWISSPROT|hyperpage}{9}
\indexentry{ID@\texttt {ID}|hyperpage}{9}
\indexentry{ID@\texttt {ID}|hyperpage}{9}
\indexentry{DE@\texttt {DE}|hyperpage}{9}
\indexentry{description!\SWISSPROT|hyperpage}{9}
\indexentry{description!\EMBL|hyperpage}{9}
\indexentry{GENBANK@\GENBANK|hyperpage}{9}
\indexentry{LOCUS@\texttt {LOCUS}|hyperpage}{9}
\indexentry{LOCUS@\texttt {LOCUS}|hyperpage}{9}
\indexentry{DEFINITION@\texttt {DEFINITION}|hyperpage}{9}
\indexentry{description!\GENBANK|hyperpage}{9}
\indexentry{ID@\texttt {ID}|hyperpage}{10}
\indexentry{LOCUS@\texttt {LOCUS}|hyperpage}{10}
\indexentry{BSSM parameter!options|hyperpage}{10}
\indexentry{speciesname\xspace @\textit {speciesname\xspace }|hyperpage}{10}
\indexentry{Option!\texttt {-species}|hyperpage}{10}
\indexentry{speciesname\xspace @\textit {speciesname\xspace }|hyperpage}{10}
\indexentry{BSSMDIR@\texttt {BSSMDIR}|hyperpage}{10}
\indexentry{BSSMDIR@\texttt {BSSMDIR}|hyperpage}{10}
\indexentry{paramfileprefix\xspace @\textit {paramfileprefix\xspace }|hyperpage}{10}
\indexentry{Option!\texttt {-bssm}|hyperpage}{10}
\indexentry{paramfileprefix\xspace @\textit {paramfileprefix\xspace }|hyperpage}{10}
\indexentry{paramfileprefix\xspace @\textit {paramfileprefix\xspace }|hyperpage}{10}
\indexentry{BSSMDIR@\texttt {BSSMDIR}|hyperpage}{10}
\indexentry{paramfile@\textit {paramfile}|hyperpage}{10}
\indexentry{scorematrixname\xspace @\textit {scorematrixname\xspace }|hyperpage}{10}
\indexentry{Option!\texttt {-scorematrix}|hyperpage}{10}
\indexentry{scorematrixname\xspace @\textit {scorematrixname\xspace }|hyperpage}{10}
\indexentry{scorematrixname\xspace @\textit {scorematrixname\xspace }|hyperpage}{10}
\indexentry{GTHDATADIR@\texttt {GTHDATADIR}|hyperpage}{10}
\indexentry{GTHDATADIR@\texttt {GTHDATADIR}|hyperpage}{10}
\indexentry{$t$@\textit {$t$}|hyperpage}{10}
\indexentry{Option!\texttt {-translationtable}|hyperpage}{10}
\indexentry{Option!\texttt {-f}|hyperpage}{12}
\indexentry{Option!\texttt {-r}|hyperpage}{12}
\indexentry{Option!\texttt {-cdnaforward}|hyperpage}{12}
\indexentry{Option!\texttt {-frompos}|hyperpage}{12}
\indexentry{Option!\texttt {-topos}|hyperpage}{12}
\indexentry{Option!\texttt {-width}|hyperpage}{12}
\indexentry{Option!\texttt {-v}|hyperpage}{13}
\indexentry{Option!\texttt {-xmlout}|hyperpage}{13}
\indexentry{Option!\texttt {-gff3out}|hyperpage}{13}
\indexentry{Option!\texttt {-md5ids}|hyperpage}{13}
\indexentry{outputfile@\textit {outputfile}|hyperpage}{13}
\indexentry{Option!\texttt {-o}|hyperpage}{13}
\indexentry{outputfile@\textit {outputfile}|hyperpage}{13}
\indexentry{Option!\texttt {-gzip}|hyperpage}{13}
\indexentry{Option!\texttt {-bzip2}|hyperpage}{13}
\indexentry{Option!\texttt {-force}|hyperpage}{13}
\indexentry{outputfile@\textit {outputfile}|hyperpage}{13}
\indexentry{outputfile@\textit {outputfile}|hyperpage}{13}
\indexentry{Option!\texttt {-skipalignmentout}|hyperpage}{13}
\indexentry{Option!\texttt {-mincutoffs}|hyperpage}{13}
\indexentry{maxintronlen\xspace @\textit {maxintronlen\xspace }|hyperpage}{13}
\indexentry{Option!\texttt {-showintronmaxlen}|hyperpage}{13}
\indexentry{maxintronlen\xspace @\textit {maxintronlen\xspace }|hyperpage}{13}
\indexentry{Option!\texttt {-minorflength}|hyperpage}{14}
\indexentry{Option!\texttt {-startcodon}|hyperpage}{14}
\indexentry{Option!\texttt {-finalstopcodon}|hyperpage}{14}
\indexentry{Option!\texttt {-showseqnums}|hyperpage}{14}
\indexentry{Option!\texttt {-pglgentemplate}|hyperpage}{14}
\indexentry{Option!\texttt {-gs2out}|hyperpage}{14}
\indexentry{outputfile@\textit {outputfile}|hyperpage}{14}
\indexentry{Option!\texttt {-maskpolyatails}|hyperpage}{14}
\indexentry{Option!\texttt {-proteinsmap}|hyperpage}{15}
\indexentry{smapfile@\textit {smapfile}|hyperpage}{15}
\indexentry{smapfile@\textit {smapfile}|hyperpage}{15}
\indexentry{Option!\texttt {-noautoindex}|hyperpage}{15}
\indexentry{Option!\texttt {-createindicesonly}|hyperpage}{15}
\indexentry{Option!\texttt {-skipindexcheck}|hyperpage}{15}
\indexentry{Option!\texttt {-minmatchlen}|hyperpage}{16}
\indexentry{Option!\texttt {-seedlength}|hyperpage}{16}
\indexentry{Option!\texttt {-exdrop}|hyperpage}{16}
\indexentry{Option!\texttt {-prminmatchlen}|hyperpage}{16}
\indexentry{Option!\texttt {-prseedlength}|hyperpage}{16}
\indexentry{Option!\texttt {-prhdist}|hyperpage}{16}
\indexentry{Option!\texttt {-online}|hyperpage}{16}
\indexentry{Option!\texttt {-inverse}|hyperpage}{16}
\indexentry{Option!\texttt {-exact}|hyperpage}{16}
\indexentry{gw@\textit {gw}|hyperpage}{17}
\indexentry{Option!\texttt {-gcmaxgapwidth}|hyperpage}{17}
\indexentry{gw@\textit {gw}|hyperpage}{17}
\indexentry{mc@\textit {mc}|hyperpage}{17}
\indexentry{Option!\texttt {-gcmincoverage}|hyperpage}{17}
\indexentry{mc@\textit {mc}|hyperpage}{17}
\indexentry{Option!\texttt {-paralogs}|hyperpage}{17}
\indexentry{mc@\textit {mc}|hyperpage}{17}
\indexentry{mc@\textit {mc}|hyperpage}{17}
\indexentry{Option!\texttt {-enrichchains}|hyperpage}{17}
\indexentry{intron cutout technique|hyperpage}{17}
\indexentry{Option!\texttt {-introncutout}|hyperpage}{17}
\indexentry{Option!\texttt {-fastdp}|hyperpage}{17}
\indexentry{s\xspace @\textit {s\xspace }|hyperpage}{17}
\indexentry{Option!\texttt {-autointroncutout}|hyperpage}{17}
\indexentry{s\xspace @\textit {s\xspace }|hyperpage}{17}
\indexentry{s\xspace @\textit {s\xspace }|hyperpage}{17}
\indexentry{d\xspace @\textit {d\xspace }|hyperpage}{17}
\indexentry{Option!\texttt {-icinitialdelta}|hyperpage}{17}
\indexentry{d\xspace @\textit {d\xspace }|hyperpage}{17}
\indexentry{d\xspace @\textit {d\xspace }|hyperpage}{17}
\indexentry{i\xspace @\textit {i\xspace }|hyperpage}{18}
\indexentry{Option!\texttt {-iciterations}|hyperpage}{18}
\indexentry{i\xspace @\textit {i\xspace }|hyperpage}{18}
\indexentry{d\xspace @\textit {d\xspace }|hyperpage}{18}
\indexentry{di\xspace @\textit {di\xspace }|hyperpage}{18}
\indexentry{d\xspace @\textit {d\xspace }|hyperpage}{18}
\indexentry{di\xspace @\textit {di\xspace }|hyperpage}{18}
\indexentry{di\xspace @\textit {di\xspace }|hyperpage}{18}
\indexentry{Option!\texttt {-icdeltaincrease}|hyperpage}{18}
\indexentry{di\xspace @\textit {di\xspace }|hyperpage}{18}
\indexentry{r\xspace @\textit {r\xspace }|hyperpage}{18}
\indexentry{Option!\texttt {-icminremintronlen}|hyperpage}{18}
\indexentry{r\xspace @\textit {r\xspace }|hyperpage}{18}
\indexentry{r\xspace @\textit {r\xspace }|hyperpage}{18}
\indexentry{Option!\texttt {-nou12intronmodel}|hyperpage}{18}
\indexentry{Option!\texttt {-u12donorprob}|hyperpage}{18}
\indexentry{Option!\texttt {-u12donorprob1mism}|hyperpage}{18}
\indexentry{Option!\texttt {-probies}|hyperpage}{19}
\indexentry{Option!\texttt {-probdelgen}|hyperpage}{19}
\indexentry{Option!\texttt {-identityweight}|hyperpage}{19}
\indexentry{Option!\texttt {-mismatchweight}|hyperpage}{19}
\indexentry{Option!\texttt {-undetcharweight}|hyperpage}{19}
\indexentry{Option!\texttt {-deletionweight}|hyperpage}{19}
\indexentry{Option!\texttt {-dpminexonlength}|hyperpage}{19}
\indexentry{Option!\texttt {-dpminintronlength}|hyperpage}{19}
\indexentry{Option!\texttt {-shortexonpenal}|hyperpage}{20}
\indexentry{Option!\texttt {-shortintronpenal}|hyperpage}{20}
\indexentry{Option!\texttt {-wzerotransition}|hyperpage}{20}
\indexentry{Option!\texttt {-wdecreasedoutput}|hyperpage}{20}
\indexentry{leadingmode\xspace @\textit {leadingmode\xspace }|hyperpage}{20}
\indexentry{Option!\texttt {-leadcutoffsmode}|hyperpage}{20}
\indexentry{leadingmode\xspace @\textit {leadingmode\xspace }|hyperpage}{20}
\indexentry{terminalmode\xspace @\textit {terminalmode\xspace }|hyperpage}{20}
\indexentry{Option!\texttt {-termcutoffsmode}|hyperpage}{20}
\indexentry{terminalmode\xspace @\textit {terminalmode\xspace }|hyperpage}{20}
\indexentry{Option!\texttt {-cutoffsminexonlen}|hyperpage}{20}
\indexentry{Option!\texttt {-scoreminexonlen}|hyperpage}{20}
\indexentry{coverage|hyperpage}{21}
\indexentry{coverage|hyperpage}{21}
\indexentry{Option!\texttt {-minalignmentscore}|hyperpage}{21}
\indexentry{Option!\texttt {-maxalignmentscore}|hyperpage}{21}
\indexentry{Option!\texttt {-mincoverage}|hyperpage}{21}
\indexentry{Option!\texttt {-maxcoverage}|hyperpage}{21}
\indexentry{Option!\texttt {-minaveragessp}|hyperpage}{21}
\indexentry{Option!\texttt {-duplicatecheck}|hyperpage}{21}
\indexentry{mode\xspace @\textit {mode\xspace }|hyperpage}{21}
\indexentry{mode\xspace @\textit {mode\xspace }|hyperpage}{22}
\indexentry{incremental updates|hyperpage}{23}
\indexentry{Option!\texttt {-intermediate}|hyperpage}{23}
\indexentry{predicted gene location|hyperpage}{23}
\indexentry{consensus spliced alignment|hyperpage}{23}
\indexentry{Option!\texttt {-sortags}|hyperpage}{23}
\indexentry{alternative gene structure|hyperpage}{23}
\indexentry{alternative gene structure!overall score|hyperpage}{23}
\indexentry{wf@\textit {wf}|hyperpage}{23}
\indexentry{Option!\texttt {-sortagswf}|hyperpage}{23}
\indexentry{wf@\textit {wf}|hyperpage}{23}
\indexentry{wf@\textit {wf}|hyperpage}{23}
\indexentry{wf@\textit {wf}|hyperpage}{23}
\indexentry{wf@\textit {wf}|hyperpage}{23}
\indexentry{Option!\texttt {-exondistri}|hyperpage}{24}
\indexentry{Option!\texttt {-introndistri}|hyperpage}{24}
\indexentry{Option!\texttt {-refseqcovdistri}|hyperpage}{24}
\indexentry{Option!\texttt {-first}|hyperpage}{24}
\indexentry{Option!\texttt {-help}|hyperpage}{24}
\indexentry{Option!\texttt {-help+}|hyperpage}{24}
\indexentry{Option!\texttt {-version}|hyperpage}{24}
\indexentry{exit code|hyperpage}{24}
\indexentry{incremental update|hyperpage}{24}
\indexentry{predicted gene structure|hyperpage}{25}
\indexentry{intermediate file|hyperpage}{25}
\indexentry{spliced alignment!consensus|hyperpage}{25}
\indexentry{predicted gene location|hyperpage}{25}
\indexentry{Option!\texttt {-alignmentscore}|hyperpage}{26}
\indexentry{Option!\texttt {-coverage}|hyperpage}{26}
\indexentry{$\Re $\xspace @\textit {$\Re $\xspace }|hyperpage}{26}
\indexentry{Option!\texttt {-range}|hyperpage}{26}
\indexentry{$\Re $\xspace @\textit {$\Re $\xspace }|hyperpage}{26}
\indexentry{$\Re $\xspace @\textit {$\Re $\xspace }|hyperpage}{26}
\indexentry{$\Re $\xspace @\textit {$\Re $\xspace }|hyperpage}{27}
\indexentry{Option!\texttt {-r}|hyperpage}{27}
\indexentry{Option!\texttt {-f}|hyperpage}{27}
\indexentry{Option!\texttt {-v}|hyperpage}{27}
\indexentry{Option!\texttt {-g}|hyperpage}{27}
\indexentry{Option!\texttt {-b}|hyperpage}{27}
\indexentry{Option!\texttt {-getcdna}|hyperpage}{28}
\indexentry{Option!\texttt {-getcdnacomp}|hyperpage}{28}
\indexentry{Option!\texttt {-getprotein}|hyperpage}{28}
\indexentry{Option!\texttt {-getproteincomp}|hyperpage}{28}
\indexentry{Option!\texttt {-getgenomic}|hyperpage}{28}
\indexentry{Option!\texttt {-getgenomiccomp}|hyperpage}{28}
\indexentry{BSSMDIR@\texttt {BSSMDIR}|hyperpage}{30}
\indexentry{dir@\textit {dir}|hyperpage}{30}
\indexentry{Option!\texttt {-outdir}|hyperpage}{30}
\indexentry{arg@\textit {arg}|hyperpage}{30}
\indexentry{Option!\texttt {-gcdonor}|hyperpage}{30}
\indexentry{type@\textit {type}|hyperpage}{30}
\indexentry{Option!\texttt {-filtertype}|hyperpage}{30}
\indexentry{n@\textit {n}|hyperpage}{31}
\indexentry{Option!\texttt {-goodexoncount}|hyperpage}{31}
\indexentry{n@\textit {n}|hyperpage}{31}
\indexentry{s@\textit {s}|hyperpage}{31}
\indexentry{Option!\texttt {-cutoff}|hyperpage}{31}
\indexentry{s@\textit {s}|hyperpage}{31}
\indexentry{type@\textit {type}|hyperpage}{31}
\indexentry{Option!\texttt {-extracttype}|hyperpage}{31}
\indexentry{file@\textit {file}|hyperpage}{31}
\indexentry{Option!\texttt {-seqfile}|hyperpage}{31}
\indexentry{file ...@\textit {file ...}|hyperpage}{31}
\indexentry{Option!\texttt {-seqfiles}|hyperpage}{31}
\indexentry{arg@\textit {arg}|hyperpage}{31}
\indexentry{Option!\texttt {-matchdesc}|hyperpage}{31}
\indexentry{arg@\textit {arg}|hyperpage}{31}
\indexentry{Option!\texttt {-usedesc}|hyperpage}{31}
\indexentry{file@\textit {file}|hyperpage}{31}
\indexentry{Option!\texttt {-regionmapping}|hyperpage}{31}
\indexentry{s@\textit {s}|hyperpage}{31}
\indexentry{Option!\texttt {-seed}|hyperpage}{31}
\indexentry{file@\textit {file}|hyperpage}{33}
\indexentry{Option!\texttt {-bssmfile}|hyperpage}{33}
\indexentry{file@\textit {file}|hyperpage}{33}
\indexentry{dir@\textit {dir}|hyperpage}{33}
\indexentry{Option!\texttt {-datapath}|hyperpage}{33}
\indexentry{dir@\textit {dir}|hyperpage}{33}
\indexentry{Option!\texttt {-gtdonor}|hyperpage}{33}
\indexentry{Option!\texttt {-gcdonor}|hyperpage}{33}
\indexentry{Option!\texttt {-agacceptor}|hyperpage}{33}
|
