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Revision: 1.1.1.1 (vendor branch)
Committed: Sat Apr 30 12:19:32 2005 UTC (11 years, 3 months ago) by maximilian
Branch: MAIN
CVS Tags: HEAD, HEAD
Changes since 1.1: +0 -0 lines
Log Message:
First import

Line File contents
1 DEBUG [main] (Startup.java:30) - Starting Jannotatix...
2 DEBUG [main] (Startup.java:31) - Current working dir is f:\max\jbproject\jannotatix
3 DEBUG [main] (Startup.java:33) - Classpath:
4 DEBUG [main] (Startup.java:37) - jannotatix.jar
5 DEBUG [main] (Config.java:46) - Init configuration
6 DEBUG [main] (Config.java:51) - loading configfileC:\Dokumente und Einstellungen\max\JannotatixPlugins\jannotatix.ini
7 2
8 DEBUG [main] (MainFrame.java:364) - Initializing Plugins
9 DEBUG [main] (AlgorithmVector.java:79) - Reading C:\Dokumente und Einstellungen\max\JannotatixPlugins\alignace.alg
10 #startElement: AlgorithmDescription
11 #characters:
12
13 #characters:
14
15
16 #startElement: Info
17 unable to find FieldDescriptor for 'Info' in ClassDescriptor of algorithm-description - ignoring extra element.
18 #characters:
19
20 #startElement: FullName
21 #characters: AlignAce - Aligns Nucleic Acids Conserved Elements
22 #endElement: FullName
23 #characters:
24
25 #startElement: Description
26 #characters: AlignAce is a Gibbs Sampler written for Yeast Genes, the original package includes sophisticated tools to rank and cluster found motifs
27 #endElement: Description
28 #characters:
29
30 #startElement: Authors
31 #characters: Roth, FR, Hughes, JD, Estep, PE, GM Church
32 #endElement: Authors
33 #characters:
34
35 #startElement: HomepageUrl
36 #characters: http://atlas.med.harvard.edu/
37 #endElement: HomepageUrl
38 #characters:
39
40 #startElement: PubmedId
41 #characters: 99788350
42 #endElement: PubmedId
43 #characters:
44
45 #startElement: ArticleFulltextUrl
46 #characters: http://arep.med.harvard.edu/pdf/Roth98.pdf
47 #endElement: ArticleFulltextUrl
48 #characters:
49
50 #startElement: Availability
51 #characters: source for Linux
52 #endElement: Availability
53 #characters:
54
55 #startElement: LicenseFilename
56 #characters: license.txt
57 #endElement: LicenseFilename
58 #characters:
59
60 #startElement: PackageUrl
61 #characters: http://atlas.med.harvard.edu/download/alignace2004.tar.gz
62 #endElement: PackageUrl
63 #characters:
64
65 #endElement: Info
66 #characters:
67
68
69 #startElement: LocalFileInvocation
70 unable to find FieldDescriptor for 'LocalFileInvocation' in ClassDescriptor of algorithm-description - ignoring extra element.
71 #characters:
72
73 #startElement: FileName
74 #characters: AlignACE
75 #endElement: FileName
76 #characters:
77
78 #startElement: FileName
79 #characters: AlignACE.exe
80 #endElement: FileName
81 #characters:
82
83 #endElement: LocalFileInvocation
84 #characters:
85
86
87 #startElement: Arguments
88 unable to find FieldDescriptor for 'Arguments' in ClassDescriptor of algorithm-description - ignoring extra element.
89 #characters:
90
91 #startElement: InfileArgument
92 #characters:
93
94 #startElement: Value
95 #endElement: Value
96 #characters:
97
98 #endElement: InfileArgument
99 #characters:
100
101
102 #startElement: OutfileArgument
103 #characters:
104
105 #startElement: Value
106 #endElement: Value
107 #characters:
108
109 #endElement: OutfileArgument
110 #characters:
111
112
113 #startElement: NumberArgument
114 #characters:
115
116 #startElement: ShortDescription
117 #characters: Width
118 #endElement: ShortDescription
119 #characters:
120
121 #startElement: Help
122 #characters: Number of columns to align (REM: This is the length/width of the motif)
123 #endElement: Help
124 #characters:
125
126 #startElement: Value
127 #endElement: Value
128 #characters:
129
130 #startElement: DefaultValue
131 #characters: 10
132 #endElement: DefaultValue
133 #characters:
134
135 #endElement: NumberArgument
136 #characters:
137
138
139 #startElement: NumberArgument
140 #characters:
141
142 #startElement: ShortDescription
143 #characters: Expected Sites
144 #endElement: ShortDescription
145 #characters:
146
147 #startElement: Value
148 #endElement: Value
149 #characters:
150
151 #startElement: DefaultValue
152 #characters: 10
153 #endElement: DefaultValue
154 #characters:
155
156 #startElement: Help
157 #characters: Number of sites expected in model
158 #endElement: Help
159 #characters:
160
161 #endElement: NumberArgument
162 #characters:
163
164
165 #startElement: NumberArgument
166 #characters:
167
168 #startElement: ShortDescription
169 #characters: GC Content
170 #endElement: ShortDescription
171 #characters:
172
173 #startElement: Value
174 #endElement: Value
175 #characters:
176
177 #startElement: DefaultValue
178 #characters: 0.38
179 #endElement: DefaultValue
180 #characters:
181
182 #startElement: Help
183 #characters: Background fractional GC content of input sequence (REM: The default value reflects the yeast genome, the value a. thaliana is 0.36)
184 #endElement: Help
185 #characters:
186
187 #endElement: NumberArgument
188 #characters:
189
190
191 #startElement: NumberArgument
192 #characters:
193
194 #startElement: ShortDescription
195 #characters: Min. Passes
196 #endElement: ShortDescription
197 #characters:
198
199 #startElement: Value
200 #endElement: Value
201 #characters:
202
203 #startElement: DefaultValue
204 #characters: 200
205 #endElement: DefaultValue
206 #characters:
207
208 #startElement: Help
209 #characters: Minimum number of non-improved passes in phase 1
210 #endElement: Help
211 #characters:
212
213 #endElement: NumberArgument
214 #characters:
215
216
217 #startElement: NumberArgument
218 #characters:
219
220 #startElement: ShortDescription
221 #characters: Oversample
222 #endElement: ShortDescription
223 #characters:
224
225 #startElement: Value
226 #endElement: Value
227 #characters:
228
229 #startElement: DefaultValue
230 #characters: 1
231 #endElement: DefaultValue
232 #characters:
233
234 #startElement: Help
235 #characters: possible sites / (expect * numcols * seedings)
236 #endElement: Help
237 #characters:
238
239 #endElement: NumberArgument
240 #characters:
241
242
243 #startElement: NumberArgument
244 #characters:
245
246 #startElement: ShortDescription
247 #characters: Undersample
248 #endElement: ShortDescription
249 #characters:
250
251 #startElement: Value
252 #endElement: Value
253 #characters:
254
255 #startElement: DefaultValue
256 #characters: 1
257 #endElement: DefaultValue
258 #characters:
259
260 #startElement: Help
261 #characters: 1/undersample
262 #endElement: Help
263 #characters:
264
265 #endElement: NumberArgument
266 #characters:
267
268 #endElement: Arguments
269 #characters:
270
271
272 #startElement: Parsers
273 unable to find FieldDescriptor for 'Parsers' in ClassDescriptor of algorithm-description - ignoring extra element.
274 #characters:
275
276 #startElement: AlignmentStartParser
277 #characters:
278
279 #startElement: Field
280 #characters: ProfileID
281 #endElement: Field
282 #characters:
283
284 #endElement: AlignmentStartParser
285 #characters:
286
287
288 #startElement: SiteParser
289 #characters:
290
291 #startElement: Field
292 #characters: SiteSequence
293 #endElement: Field
294 #characters:
295
296 #startElement: Field
297 #characters: SequenceNumber
298 #endElement: Field
299 #characters:
300
301 #startElement: Field
302 #characters: Start
303 #endElement: Field
304 #characters:
305
306 #startElement: Field
307 #characters: Strand
308 #endElement: Field
309 #characters:
310
311 #endElement: SiteParser
312 #characters:
313
314
315 #startElement: AlignmentEndParser
316 #characters:
317
318 #startElement: Field
319 #characters: ProfileScore_MAP
320 #endElement: Field
321 #characters:
322
323 #endElement: AlignmentEndParser
324 #characters:
325
326 #endElement: Parsers
327 #characters:
328
329
330 #endElement: AlgorithmDescription
331 DEBUG [main] (AlgorithmVector.java:81) - Algorithm nullloaded
332 DEBUG [main] (AlgorithmVector.java:79) - Reading C:\Dokumente und Einstellungen\max\JannotatixPlugins\meme.alg
333 #startElement: AlgorithmDescription
334 #characters:
335
336 #characters:
337
338
339 #startElement: Info
340 unable to find FieldDescriptor for 'Info' in ClassDescriptor of algorithm-description - ignoring extra element.
341 #characters:
342
343 #startElement: Description
344 #characters: Multiple EM for Motif Elicitation
345 #endElement: Description
346 #characters:
347
348 #startElement: Authors
349 #characters: Timothy Bailey, Charles Elkan, Bill Grundy
350 #endElement: Authors
351 #characters:
352
353 #startElement: HomepageUrl
354 #characters: http://meme.sdsc.edu
355 #endElement: HomepageUrl
356 #characters:
357
358 #startElement: PubmedId
359 #characters: 7584402
360 #endElement: PubmedId
361 #characters:
362
363 #startElement: ArticleFulltextUrl
364 #characters: http://www.sdsc.edu/~tbailey/papers/ismb94.ps
365 #endElement: ArticleFulltextUrl
366 #characters:
367
368 #startElement: Availability
369 #characters: web / sourcecode for unix
370 #endElement: Availability
371 #characters:
372
373 #startElement: LicenseFilename
374 #characters: Meme/COPYRIGHT
375 #endElement: LicenseFilename
376 #characters:
377
378 #startElement: PackageUrl
379 #endElement: PackageUrl
380 #characters:
381
382 #startElement: PackageUrl
383 #characters: ftp://ftp.sdsc.edu/pub/sdsc/biology/meme/meme.3.0.4.tar.Z
384 #endElement: PackageUrl
385 #characters:
386
387 #endElement: Info
388 #characters:
389
390
391 #startElement: LocalFileInvocation
392 unable to find FieldDescriptor for 'LocalFileInvocation' in ClassDescriptor of algorithm-description - ignoring extra element.
393 #characters:
394
395 #startElement: FileName
396 #characters: meme-linux/bin/meme
397 #endElement: FileName
398 #characters:
399
400 #startElement: FileName
401 #endElement: FileName
402 #characters:
403
404 #endElement: LocalFileInvocation
405 #characters:
406
407
408 #startElement: Arguments
409 unable to find FieldDescriptor for 'Arguments' in ClassDescriptor of algorithm-description - ignoring extra element.
410 #characters:
411
412
413 #startElement: InfileArgument
414 #characters:
415
416 #endElement: InfileArgument
417 #characters:
418
419
420 #startElement: OutfileArgument
421 #characters:
422
423 #startElement: Value
424 #characters: STDOUT
425 #endElement: Value
426 #characters:
427
428 #endElement: OutfileArgument
429 #characters:
430
431
432 #startElement: ListArgument
433 #characters:
434
435 #startElement: ShortDescription
436 #characters: Distribution of motifs
437 #endElement: ShortDescription
438 #characters:
439
440 #startElement: Help
441 #characters: One Occurrence Per Sequence (oops), Zero or One Occurrence Per Sequence (zoops) or Two-Component Mixture (tcm)
442 #endElement: Help
443 #characters:
444
445 #startElement: Value
446 #endElement: Value
447 #characters:
448
449 #startElement: PossibleValue
450 #characters: oops
451 #endElement: PossibleValue
452 #characters:
453
454 #startElement: PossibleValue
455 #characters: zoops
456 #endElement: PossibleValue
457 #characters:
458
459 #startElement: PossibleValue
460 #characters: tcm
461 #endElement: PossibleValue
462 #characters:
463
464 #startElement: DefaultValue
465 #characters: zoops
466 #endElement: DefaultValue
467 #characters:
468
469 #endElement: ListArgument
470 #characters:
471
472
473 #startElement: NumberArgument
474 #characters:
475
476 #startElement: ShortDescription
477 #characters: Maximum number of motifs
478 #endElement: ShortDescription
479 #characters:
480
481 #startElement: Value
482 #endElement: Value
483 #characters:
484
485 #startElement: DefaultValue
486 #characters: 1
487 #endElement: DefaultValue
488 #characters:
489
490 #startElement: Help
491 #characters: The number of *different* motifs to search for
492 #endElement: Help
493 #characters:
494
495 #endElement: NumberArgument
496 #characters:
497
498
499 #startElement: NumberArgument
500 #characters:
501
502 #startElement: ShortDescription
503 #characters: Number of sites
504 #endElement: ShortDescription
505 #characters:
506
507 #startElement: Value
508 #endElement: Value
509 #characters:
510
511 #startElement: DefaultValue
512 #characters: 1
513 #endElement: DefaultValue
514 #characters:
515
516 #startElement: Help
517 #characters: The (expected) number of occurrences of each motif. If -nsites is given, only that number of occurrences is tried.
518 These switches are ignored if mod = oops.
519 #endElement: Help
520 #characters:
521
522 #endElement: NumberArgument
523 #characters:
524
525
526 #startElement: NumberArgument
527 #characters:
528
529 #startElement: ShortDescription
530 #characters: Minimal Width
531 #endElement: ShortDescription
532 #characters:
533
534 #startElement: Value
535 #endElement: Value
536 #characters:
537
538 #startElement: DefaultValue
539 #characters: 8
540 #endElement: DefaultValue
541 #characters:
542
543 #startElement: Help
544 #characters: Minimal width of the motif to try
545 #endElement: Help
546 #characters:
547
548 #endElement: NumberArgument
549 #characters:
550
551
552 #startElement: NumberArgument
553 #characters:
554
555 #startElement: ShortDescription
556 #characters: Maximal Width
557 #endElement: ShortDescription
558 #characters:
559
560 #startElement: Value
561 #endElement: Value
562 #characters:
563
564 #startElement: DefaultValue
565 #characters: 25
566 #endElement: DefaultValue
567 #characters:
568
569 #startElement: Help
570 #characters: Maximal width of the motif to try
571 #endElement: Help
572 #characters:
573
574 #endElement: NumberArgument
575 #characters:
576
577
578 #startElement: FileArgument
579 #characters:
580
581 #startElement: ShortDescription
582 #characters: Background Model
583 #endElement: ShortDescription
584 #characters:
585
586 #startElement: Value
587 #endElement: Value
588 #characters:
589
590 #startElement: DefaultValue
591 #endElement: DefaultValue
592 #characters:
593
594 #startElement: Help
595 #characters: The name of the file containing the background model for sequences.
596 #endElement: Help
597 #characters:
598
599 #endElement: FileArgument
600 #characters:
601
602
603 #startElement: NumberArgument
604 #characters:
605
606 #startElement: ShortDescription
607 #characters: Max Iterations
608 #endElement: ShortDescription
609 #characters:
610
611 #startElement: Value
612 #endElement: Value
613 #characters:
614
615 #startElement: DefaultValue
616 #characters: 50
617 #endElement: DefaultValue
618 #characters:
619
620 #startElement: Help
621 #characters: The number of iterations of EM to run from any starting point.
622 #endElement: Help
623 #characters:
624
625 #endElement: NumberArgument
626 #characters:
627
628
629 #startElement: OptionalArgument
630 #characters:
631
632 #startElement: ShortDescription
633 #characters: Look on reverse strand
634 #endElement: ShortDescription
635 #characters:
636
637 #startElement: Value
638 #endElement: Value
639 #characters:
640
641 #startElement: DefaultValue
642 #characters: false
643 #endElement: DefaultValue
644 #characters:
645
646 #startElement: Help
647 #characters: motifs occurrences may be on the given DNA strand
648 or on its reverse complement.
649 Default: look for DNA motifs only on the strand given
650 in the training set.
651 #endElement: Help
652 #characters:
653
654 #endElement: OptionalArgument
655 #characters:
656
657
658 #startElement: OptionalArgument
659 #characters:
660
661 #startElement: ShortDescription
662 #characters: Look for palindromes
663 #endElement: ShortDescription
664 #characters:
665
666 #startElement: Value
667 #endElement: Value
668 #characters:
669
670 #startElement: DefaultValue
671 #characters: false
672 #endElement: DefaultValue
673 #characters:
674
675 #startElement: Help
676 #characters: Choosing -pal causes MEME to look for palindromes in
677 DNA datasets.
678 #characters: <
679 #characters: p
680 #characters: >
681 #characters:
682 MEME averages the letter frequencies in corresponding
683 columns of the motif (PSPM) together. For instance,
684 if the width of the motif is 10, columns 1 and 10, 2
685 and 9, 3 and 8, etc., are averaged together. The
686 averaging combines the frequency of A in one column
687 with T in the other, and the frequency of C in one
688 column with G in the other.
689 #endElement: Help
690 #characters:
691
692 #endElement: OptionalArgument
693 #characters:
694
695
696 #startElement: ListArgument
697 #characters:
698
699 #startElement: ShortDescription
700 #characters: Distribution of prior
701 #endElement: ShortDescription
702 #characters:
703
704 #startElement: Help
705 #characters: The prior distribution on the model parameters:
706 #characters: <
707 #characters: p
708 #characters: >
709 #characters:
710 dirichlet == simple Dirichlet prior
711 This is the default for -dna and
712 -alph. It is based on the
713 non-redundant database letter
714 frequencies.
715 #characters: <
716 #characters: p
717 #characters: >
718 #characters:
719 dmix == mixture of Dirichlets prior. This is the default for -protein.
720 #characters: <
721 #characters: p
722 #characters: >
723 #characters:
724 mega == extremely low variance dmix; variance is scaled inversely with the size of the dataset.
725 #characters: <
726 #characters: p
727 #characters: >
728 #characters:
729 megap == mega for all but last iteration of EM; dmix on last iteration.
730 #characters: <
731 #characters: p
732 #characters: >
733 #characters:
734 addone == add +1 to each observed count
735 #characters: <
736 #characters: p
737 #characters: >
738 #endElement: Help
739 #characters:
740
741 #startElement: Value
742 #endElement: Value
743 #characters:
744
745 #startElement: PossibleValue
746 #characters: dirichlet
747 #endElement: PossibleValue
748 #characters:
749
750 #startElement: PossibleValue
751 #characters: dmix
752 #endElement: PossibleValue
753 #characters:
754
755 #startElement: PossibleValue
756 #characters: mega
757 #endElement: PossibleValue
758 #characters:
759
760 #startElement: PossibleValue
761 #characters: megap
762 #endElement: PossibleValue
763 #characters:
764
765 #startElement: PossibleValue
766 #characters: addone
767 #endElement: PossibleValue
768 #characters:
769
770 #startElement: DefaultValue
771 #characters: dirichlet
772 #endElement: DefaultValue
773 #characters:
774
775 #endElement: ListArgument
776 #characters:
777
778
779 #startElement: ConstantArgument
780 #characters:
781
782 #startElement: ShortDescription
783 #characters: skip strange matrix trimming steps
784 #endElement: ShortDescription
785 #characters:
786
787 #endElement: ConstantArgument
788 #characters:
789
790
791 #startElement: ConstantArgument
792 #characters:
793
794 #startElement: ShortDescription
795 #characters: Output as Text
796 #endElement: ShortDescription
797 #characters:
798
799 #endElement: ConstantArgument
800 #characters:
801
802
803 #startElement: ConstantArgument
804 #characters:
805
806 #startElement: ShortDescription
807 #characters: Assume DNA alphabet
808 #endElement: ShortDescription
809 #characters:
810
811 #endElement: ConstantArgument
812 #characters:
813
814
815 #startElement: ConstantArgument
816 #characters:
817
818 #startElement: ShortDescription
819 #characters: Print motifs in fasta format
820 #endElement: ShortDescription
821 #characters:
822
823 #endElement: ConstantArgument
824 #characters:
825
826
827 #endElement: Arguments
828 #characters:
829
830
831 #startElement: Parsers
832 unable to find FieldDescriptor for 'Parsers' in ClassDescriptor of algorithm-description - ignoring extra element.
833 #characters:
834
835 #startElement: AlignmentStartParser
836 #characters:
837
838 #startElement: Field
839 #characters: AlignmentID
840 #endElement: Field
841 #characters:
842
843 #endElement: AlignmentStartParser
844 #characters:
845
846
847 #startElement: AlignmentStartParser
848 #characters:
849
850 #startElement: Field
851 #characters: Ignore
852 #endElement: Field
853 #characters:
854
855 #endElement: AlignmentStartParser
856 #characters:
857
858
859 #startElement: AlignmentStartParser
860 #characters:
861
862 #startElement: Field
863 #characters: Ignore
864 #endElement: Field
865 #characters:
866
867 #endElement: AlignmentStartParser
868 #characters:
869
870
871 #startElement: SiteParser
872 #characters:
873
874 #startElement: Field
875 #characters: Sequence
876 #endElement: Field
877 #characters:
878
879 #endElement: SiteParser
880 #characters:
881
882
883 #startElement: SiteParser
884 #characters:
885
886 #startElement: Field
887 #characters: Start
888 #endElement: Field
889 #characters:
890
891 #startElement: Field
892 #characters: Score
893 #endElement: Field
894 #characters:
895
896 #startElement: Field
897 #characters: SiteSequence
898 #endElement: Field
899 #characters:
900
901 #endElement: SiteParser
902 #characters:
903
904
905 #startElement: AlignmentEndParser
906 #characters:
907
908 #endElement: AlignmentEndParser
909 #characters:
910
911 #endElement: Parsers
912 #characters:
913
914
915 #endElement: AlgorithmDescription
916 DEBUG [main] (AlgorithmVector.java:81) - Algorithm nullloaded
917 DEBUG [main] (AlgorithmVector.java:79) - Reading C:\Dokumente und Einstellungen\max\JannotatixPlugins\motifsampler.alg
918 #startElement: AlgorithmDescription
919 #characters:
920
921 #characters:
922
923
924
925 #startElement: Info
926 unable to find FieldDescriptor for 'Info' in ClassDescriptor of algorithm-description - ignoring extra element.
927 #characters:
928
929 #startElement: FullName
930 #characters: MotifSampler
931 #endElement: FullName
932 #characters:
933
934 #startElement: Description
935 #characters: Motif Sampler is a Gibbs Motif Sampler from the PlantCare
936 team
937 #endElement: Description
938 #characters:
939
940 #startElement: Authors
941 #characters: Thijs G., Lescot M., Marchal K., Rombauts S., De Moor B.,
942 Rouze P., Moreau Y.
943 #endElement: Authors
944 #characters:
945
946 #startElement: HomepageUrl
947 #characters: http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html
948 #endElement: HomepageUrl
949 #characters:
950
951 #startElement: PubmedId
952 #characters: 11751219
953 #endElement: PubmedId
954 #characters:
955
956 #startElement: ArticleFulltextUrl
957 #characters: http://bioinformatics.oupjournals.org/cgi/reprint/17/12/1113
958 #endElement: ArticleFulltextUrl
959 #characters:
960
961 #startElement: Availability
962 #characters: web / binary for Linux and Windows
963 #endElement: Availability
964 #characters:
965
966 #startElement: LicenseFilename
967 #endElement: LicenseFilename
968 #characters:
969
970 #startElement: PackageUrl
971 #characters: http://www.esat.kuleuven.ac.be/~thijs/download/windows/MotifSampler.exe
972 #endElement: PackageUrl
973 #characters:
974
975 #startElement: PackageUrl
976 #characters: http://www.esat.kuleuven.ac.be/~thijs/download/linux_3.0/MotifSampler
977 #endElement: PackageUrl
978 #characters:
979
980 #endElement: Info
981 #characters:
982
983
984 #startElement: LocalFileInvocation
985 unable to find FieldDescriptor for 'LocalFileInvocation' in ClassDescriptor of algorithm-description - ignoring extra element.
986 #characters:
987
988 #startElement: FileName
989 #characters: MotifSampler
990 #endElement: FileName
991 #characters:
992
993
994 #startElement: FileName
995 #characters: MotifSampler.exe
996 #endElement: FileName
997 #characters:
998
999 #endElement: LocalFileInvocation
1000 #characters:
1001
1002
1003 #startElement: Arguments
1004 unable to find FieldDescriptor for 'Arguments' in ClassDescriptor of algorithm-description - ignoring extra element.
1005 #characters:
1006
1007 #startElement: InfileArgument
1008 #characters:
1009
1010 #startElement: Value
1011 #endElement: Value
1012 #characters:
1013
1014 #endElement: InfileArgument
1015 #characters:
1016
1017
1018 #startElement: OutfileArgument
1019 #characters:
1020
1021 #startElement: Value
1022 #endElement: Value
1023 #characters:
1024
1025 #endElement: OutfileArgument
1026 #characters:
1027
1028
1029 #startElement: NumberArgument
1030 #characters:
1031
1032 #startElement: ShortDescription
1033 #characters: Width
1034 #endElement: ShortDescription
1035 #characters:
1036
1037
1038 #startElement: Help
1039 #characters: The exact width of the motif has to be known in advance!
1040 #endElement: Help
1041 #characters:
1042
1043
1044 #startElement: Value
1045 #endElement: Value
1046 #characters:
1047
1048
1049 #startElement: DefaultValue
1050 #characters: 8
1051 #endElement: DefaultValue
1052 #characters:
1053
1054 #endElement: NumberArgument
1055 #characters:
1056
1057
1058 #startElement: FileArgument
1059 #characters:
1060
1061 #startElement: ShortDescription
1062 #characters: Background Model
1063 #endElement: ShortDescription
1064 #characters:
1065
1066
1067 #startElement: Value
1068 #endElement: Value
1069 #characters:
1070
1071
1072 #startElement: DefaultValue
1073 #characters: athaliana_3.bg
1074 #endElement: DefaultValue
1075 #characters:
1076
1077
1078 #startElement: Help
1079 #characters: A hidden markov model that estimates the probability that a given
1080 sequence is produced by intergenic-sequence noise
1081 #endElement: Help
1082 #characters:
1083
1084 #endElement: FileArgument
1085 #characters:
1086
1087
1088 #startElement: ListArgument
1089 #characters:
1090
1091 #startElement: ShortDescription
1092 #characters: Strand
1093 #endElement: ShortDescription
1094 #characters:
1095
1096
1097 #startElement: Help
1098 #characters: Search both (1) or only one strand (0)
1099 #endElement: Help
1100 #characters:
1101
1102
1103 #startElement: Value
1104 #endElement: Value
1105 #characters:
1106
1107
1108 #startElement: PossibleValue
1109 #characters: 0
1110 #endElement: PossibleValue
1111 #characters:
1112
1113
1114 #startElement: PossibleValue
1115 #characters: 1
1116 #endElement: PossibleValue
1117 #characters:
1118
1119
1120 #startElement: DefaultValue
1121 #characters: 1
1122 #endElement: DefaultValue
1123 #characters:
1124
1125 #endElement: ListArgument
1126 #characters:
1127
1128
1129 #startElement: NumberArgument
1130 #characters:
1131
1132 #startElement: ShortDescription
1133 #characters: Prior
1134 #endElement: ShortDescription
1135 #characters:
1136
1137
1138 #startElement: Value
1139 #endElement: Value
1140 #characters:
1141
1142
1143 #startElement: DefaultValue
1144 #characters: 0.2
1145 #endElement: DefaultValue
1146 #characters:
1147
1148
1149 #startElement: Help
1150 #characters: The a priori probability that a sequence contains a motif
1151 #endElement: Help
1152 #characters:
1153
1154 #endElement: NumberArgument
1155 #characters:
1156
1157
1158 #startElement: NumberArgument
1159 #characters:
1160
1161 #startElement: ShortDescription
1162 #characters: Max. Instances
1163 #endElement: ShortDescription
1164 #characters:
1165
1166
1167 #startElement: Value
1168 #endElement: Value
1169 #characters:
1170
1171
1172 #startElement: DefaultValue
1173 #characters: 0
1174 #endElement: DefaultValue
1175 #characters:
1176
1177
1178 #startElement: Help
1179 #characters: Maximum number of instances or 0 to deactivate limit
1180 #endElement: Help
1181 #characters:
1182
1183 #endElement: NumberArgument
1184 #characters:
1185
1186
1187 #startElement: NumberArgument
1188 #characters:
1189
1190 #startElement: ShortDescription
1191 #characters: Number of Motifs
1192 #endElement: ShortDescription
1193 #characters:
1194
1195
1196 #startElement: Value
1197 #endElement: Value
1198 #characters:
1199
1200
1201 #startElement: DefaultValue
1202 #characters: 4
1203 #endElement: DefaultValue
1204 #characters:
1205
1206
1207 #startElement: Help
1208 #characters: Number of motifs to search for
1209 #endElement: Help
1210 #characters:
1211
1212 #endElement: NumberArgument
1213 #characters:
1214
1215
1216 #startElement: NumberArgument
1217 #characters:
1218
1219 #startElement: ShortDescription
1220 #characters: Iterations
1221 #endElement: ShortDescription
1222 #characters:
1223
1224 #startElement: Value
1225 #endElement: Value
1226 #characters:
1227
1228 #startElement: DefaultValue
1229 #characters: 1
1230 #endElement: DefaultValue
1231 #characters:
1232
1233 #startElement: Help
1234 #characters: Number of iterations, the algorithm is simply repeated this number
1235 of times
1236 #endElement: Help
1237 #characters:
1238
1239 #endElement: NumberArgument
1240 #characters:
1241
1242 #endElement: Arguments
1243 #characters:
1244
1245
1246 #startElement: Parsers
1247 unable to find FieldDescriptor for 'Parsers' in ClassDescriptor of algorithm-description - ignoring extra element.
1248 #characters:
1249
1250 #startElement: SiteParser
1251 #characters:
1252
1253 #startElement: Field
1254 #characters: Sequence
1255 #endElement: Field
1256 #characters:
1257
1258
1259 #startElement: Field
1260 #characters: Source
1261 #endElement: Field
1262 #characters:
1263
1264
1265 #startElement: Field
1266 #characters: Start
1267 #endElement: Field
1268 #characters:
1269
1270
1271 #startElement: Field
1272 #characters: End
1273 #endElement: Field
1274 #characters:
1275
1276
1277 #startElement: Field
1278 #characters: Score
1279 #endElement: Field
1280 #characters:
1281
1282
1283 #startElement: Field
1284 #characters: Strand
1285 #endElement: Field
1286 #characters:
1287
1288
1289 #startElement: Field
1290 #characters: ProfileID
1291 #endElement: Field
1292 #characters:
1293
1294 #endElement: SiteParser
1295 #characters:
1296
1297 #endElement: Parsers
1298 #characters:
1299
1300 #endElement: AlgorithmDescription
1301 DEBUG [main] (AlgorithmVector.java:81) - Algorithm nullloaded
1302 DEBUG [main] (AlgorithmVector.java:79) - Reading C:\Dokumente und Einstellungen\max\JannotatixPlugins\plantcare.alg
1303 #startElement: AlgorithmDescription
1304 #characters:
1305
1306
1307 #startElement: Info
1308 unable to find FieldDescriptor for 'Info' in ClassDescriptor of algorithm-description - ignoring extra element.
1309 #characters:
1310
1311 #startElement: FullName
1312 #characters: PlantCare
1313 #endElement: FullName
1314 #characters:
1315
1316 #startElement: Description
1317 #characters: Plantcare is a database of plant cis-acting regulatory elements, many of them from Arabidopsis
1318 #endElement: Description
1319 #characters:
1320
1321 #startElement: Authors
1322 #characters: Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P, Rombauts S.
1323 #endElement: Authors
1324 #characters:
1325
1326 #startElement: HomepageUrl
1327 #characters: http://oberon.fvms.ugent.be:8080/PlantCARE/index.html
1328 #endElement: HomepageUrl
1329 #characters:
1330
1331 #startElement: PubmedId
1332 #characters: 11752327
1333 #endElement: PubmedId
1334 #characters:
1335
1336 #startElement: ArticleFulltextUrl
1337 #characters: http://www.ncbi.nlm.nih.gov/fullTEXT
1338 #endElement: ArticleFulltextUrl
1339 #characters:
1340
1341 #startElement: Availability
1342 #characters: website
1343 #endElement: Availability
1344 #characters:
1345
1346 #startElement: LicenseFilename
1347 #endElement: LicenseFilename
1348 #characters:
1349
1350 #endElement: Info
1351 #characters:
1352
1353
1354 #startElement: HttpPostInvocation
1355 unable to find FieldDescriptor for 'HttpPostInvocation' in ClassDescriptor of algorithm-description - ignoring extra element.
1356 #characters:
1357
1358 #startElement: Description
1359 #characters: PlantCare Main Server
1360 #endElement: Description
1361 #characters:
1362
1363 #startElement: Url
1364 #characters: http://oberon.fvms.ugent.be:8080/care-bin/CallMat_NN47.htpl
1365 #endElement: Url
1366 #characters:
1367
1368 #startElement: HttpAuthLogin
1369 #characters:
1370
1371 #startElement: Username
1372 #characters: me
1373 #endElement: Username
1374 #characters:
1375
1376 #startElement: Password
1377 #characters: Test
1378 #endElement: Password
1379 #characters:
1380
1381 #endElement: HttpAuthLogin
1382 #characters:
1383
1384 #endElement: HttpPostInvocation
1385 #characters:
1386
1387
1388 #startElement: Arguments
1389 unable to find FieldDescriptor for 'Arguments' in ClassDescriptor of algorithm-description - ignoring extra element.
1390 #characters:
1391
1392 #startElement: InfileArgument
1393 #characters:
1394
1395 #startElement: Value
1396 #endElement: Value
1397 #characters:
1398
1399 #endElement: InfileArgument
1400 #characters:
1401
1402
1403 #startElement: ConstantArgument
1404 #characters:
1405
1406 #startElement: ShortDescription
1407 #characters: This parameter has to be specified
1408 #endElement: ShortDescription
1409 #characters:
1410
1411 #startElement: DefaultValue
1412 #endElement: DefaultValue
1413 #characters:
1414
1415 #startElement: Value
1416 #characters: Search
1417 #endElement: Value
1418 #characters:
1419
1420 #endElement: ConstantArgument
1421 #characters:
1422
1423
1424 #endElement: Arguments
1425 #characters:
1426
1427
1428 #startElement: Parsers
1429 unable to find FieldDescriptor for 'Parsers' in ClassDescriptor of algorithm-description - ignoring extra element.
1430 #characters:
1431
1432 #startElement: AlignmentStartParser
1433 #characters:
1434
1435 #startElement: Field
1436 #characters: Name
1437 #endElement: Field
1438 #characters:
1439
1440 #endElement: AlignmentStartParser
1441 #characters:
1442
1443
1444 #startElement: SiteParser
1445 #characters:
1446
1447 #startElement: Field
1448 #characters: Organism
1449 #endElement: Field
1450 #characters:
1451
1452 #endElement: SiteParser
1453 #characters:
1454
1455
1456 #startElement: SiteParser
1457 #characters:
1458
1459 #startElement: Field
1460 #characters: Start
1461 #endElement: Field
1462 #characters:
1463
1464 #endElement: SiteParser
1465 #characters:
1466
1467
1468 #startElement: SiteParser
1469 #characters:
1470
1471 #startElement: Field
1472 #characters: Strand
1473 #endElement: Field
1474 #characters:
1475
1476 #endElement: SiteParser
1477 #characters:
1478
1479
1480 #startElement: SiteParser
1481 #characters:
1482
1483 #startElement: Field
1484 #characters: Core_Score
1485 #endElement: Field
1486 #characters:
1487
1488 #endElement: SiteParser
1489 #characters:
1490
1491
1492 #startElement: SiteParser
1493 #characters:
1494
1495 #startElement: Field
1496 #characters: Score
1497 #endElement: Field
1498 #characters:
1499
1500 #endElement: SiteParser
1501 #characters:
1502
1503
1504 #startElement: SiteParser
1505 #characters:
1506
1507 #startElement: Field
1508 #characters: SiteSequence
1509 #endElement: Field
1510 #characters:
1511
1512 #endElement: SiteParser
1513 #characters:
1514
1515
1516 #startElement: AlignmentEndParser
1517 #characters:
1518
1519 #startElement: Field
1520 #characters: Function
1521 #endElement: Field
1522 #characters:
1523
1524 #endElement: AlignmentEndParser
1525 #characters:
1526
1527
1528 #endElement: Parsers
1529 #characters:
1530
1531 #endElement: AlgorithmDescription
1532 DEBUG [main] (AlgorithmVector.java:81) - Algorithm nullloaded
1533 DEBUG [main] (AlgorithmVector.java:79) - Reading C:\Dokumente und Einstellungen\max\JannotatixPlugins\transfac.alg
1534 #startElement: AlgorithmDescription
1535 #characters:
1536
1537
1538 #startElement: Info
1539 unable to find FieldDescriptor for 'Info' in ClassDescriptor of algorithm-description - ignoring extra element.
1540 #characters:
1541
1542 #startElement: FullName
1543 #characters: Match using Transfac public
1544 #endElement: FullName
1545 #characters:
1546
1547 #startElement: Description
1548 #characters: Match uses matrices from Transfac public 6.0
1549 #endElement: Description
1550 #characters:
1551
1552 #startElement: Authors
1553 #characters: Biobase.de
1554 #endElement: Authors
1555 #characters:
1556
1557 #startElement: HomepageUrl
1558 #characters: http://www.gene-regulation.com
1559 #endElement: HomepageUrl
1560 #characters:
1561
1562 #startElement: ManualUrl
1563 #characters: http://www.gene-regulation.com/pub/programs/match/help_match.htm
1564 #endElement: ManualUrl
1565 #characters:
1566
1567 #startElement: PubmedId
1568 #characters: 11125113
1569 #endElement: PubmedId
1570 #characters:
1571
1572 #startElement: ArticleFulltextUrl
1573 #characters: http://nar.oupjournals.org/cgi/content/full/29/1/281
1574 #endElement: ArticleFulltextUrl
1575 #characters:
1576
1577 #startElement: Availability
1578 #characters: Website
1579 #endElement: Availability
1580 #characters:
1581
1582 #startElement: LicenseFilename
1583 #endElement: LicenseFilename
1584 #characters:
1585
1586 #endElement: Info
1587 #characters:
1588
1589
1590 #startElement: HttpPostInvocation
1591 unable to find FieldDescriptor for 'HttpPostInvocation' in ClassDescriptor of algorithm-description - ignoring extra element.
1592 #characters:
1593
1594 #startElement: Description
1595 #characters: Match server on www.gene-regulation.com
1596 #endElement: Description
1597 #characters:
1598
1599 #startElement: Url
1600 #characters: http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi
1601 #endElement: Url
1602 #characters:
1603
1604 #startElement: CookieLogin
1605 #characters:
1606
1607 #startElement: CookiePageUrl
1608 #characters: http://www.gene-regulation.com/login
1609 #endElement: CookiePageUrl
1610 #characters:
1611
1612 #startElement: Username
1613 #characters: maximilianh
1614 #endElement: Username
1615 #characters:
1616
1617 #startElement: Password
1618 #characters: testqwe
1619 #endElement: Password
1620 #characters:
1621
1622 #startElement: SendHiddenParameter
1623 #characters: /index.html
1624 #endElement: SendHiddenParameter
1625 #characters:
1626
1627 #endElement: CookieLogin
1628 #characters:
1629
1630 #endElement: HttpPostInvocation
1631 #characters:
1632
1633
1634 #startElement: Arguments
1635 unable to find FieldDescriptor for 'Arguments' in ClassDescriptor of algorithm-description - ignoring extra element.
1636 #characters:
1637
1638
1639 #startElement: ConstantArgument
1640 #characters:
1641
1642 #startElement: ShortDescription
1643 #characters: Type of search, this is the first search
1644 #endElement: ShortDescription
1645 #characters:
1646
1647 #startElement: Value
1648 #characters: First
1649 #endElement: Value
1650 #characters:
1651
1652 #endElement: ConstantArgument
1653 #characters:
1654
1655
1656 #startElement: ConstantArgument
1657 #characters:
1658
1659 #startElement: ShortDescription
1660 #characters: Name of the search
1661 #endElement: ShortDescription
1662 #characters:
1663
1664 #startElement: Value
1665 #characters: default
1666 #endElement: Value
1667 #characters:
1668
1669 #endElement: ConstantArgument
1670 #characters:
1671
1672
1673 #startElement: ConstantArgument
1674 #characters:
1675
1676 #startElement: ShortDescription
1677 #characters: no idea
1678 #endElement: ShortDescription
1679 #characters:
1680
1681 #startElement: Value
1682 #characters: default.seq
1683 #endElement: Value
1684 #characters:
1685
1686 #endElement: ConstantArgument
1687 #characters:
1688
1689
1690 #startElement: ConstantArgument
1691 #characters:
1692
1693 #startElement: ShortDescription
1694 #characters: What the heck is this?
1695 #endElement: ShortDescription
1696 #characters:
1697
1698 #startElement: Value
1699 #characters: DEL
1700 #endElement: Value
1701 #characters:
1702
1703 #endElement: ConstantArgument
1704 #characters:
1705
1706
1707 #startElement: ConstantArgument
1708 #characters:
1709
1710 #startElement: ShortDescription
1711 #characters: Name of the sequence
1712 #endElement: ShortDescription
1713 #characters:
1714
1715 #startElement: Value
1716 #characters: default
1717 #endElement: Value
1718 #characters:
1719
1720 #endElement: ConstantArgument
1721 #characters:
1722
1723
1724 #startElement: InfileArgument
1725 #characters:
1726
1727 #endElement: InfileArgument
1728 #characters:
1729
1730
1731 #startElement: ListArgument
1732 #characters:
1733
1734 #startElement: ShortDescription
1735 #characters: Search matrices or profiles?
1736 #endElement: ShortDescription
1737 #characters:
1738
1739 #startElement: Help
1740 #characters: Instead of selecting a larger group of matrices, you can also use a
1741 predefined profile. Each profile includes a subset of matrices
1742 with defined cut-offs
1743 #endElement: Help
1744 #characters:
1745
1746 #startElement: Value
1747 #characters: ALL
1748 #endElement: Value
1749 #characters:
1750
1751 #startElement: PossibleValue
1752 #characters: ALL
1753 #endElement: PossibleValue
1754 #characters:
1755
1756 #startElement: PossibleValue
1757 #characters: PRF
1758 #endElement: PossibleValue
1759 #characters:
1760
1761 #startElement: DefaultValue
1762 #characters: ALL
1763 #endElement: DefaultValue
1764 #characters:
1765
1766 #endElement: ListArgument
1767 #characters:
1768
1769
1770 #startElement: ListArgument
1771 #characters:
1772
1773 #startElement: ShortDescription
1774 #characters: If matrix: Group of matrices
1775 #endElement: ShortDescription
1776 #characters:
1777
1778 #startElement: Value
1779 #characters: all
1780 #endElement: Value
1781 #characters:
1782
1783 #startElement: PossibleValue
1784 #characters: all
1785 #endElement: PossibleValue
1786 #characters:
1787
1788 #startElement: PossibleValue
1789 #characters: vertebrates
1790 #endElement: PossibleValue
1791 #characters:
1792
1793 #startElement: PossibleValue
1794 #characters: fungi
1795 #endElement: PossibleValue
1796 #characters:
1797
1798 #startElement: PossibleValue
1799 #characters: plants
1800 #endElement: PossibleValue
1801 #characters:
1802
1803 #startElement: PossibleValue
1804 #characters: insects
1805 #endElement: PossibleValue
1806 #characters:
1807
1808 #startElement: PossibleValue
1809 #characters: nematodes
1810 #endElement: PossibleValue
1811 #characters:
1812
1813 #startElement: PossibleValue
1814 #characters: bacteria
1815 #endElement: PossibleValue
1816 #characters:
1817
1818 #startElement: DefaultValue
1819 #characters: all
1820 #endElement: DefaultValue
1821 #characters:
1822
1823 #endElement: ListArgument
1824 #characters:
1825
1826
1827 #startElement: OptionalArgument
1828 #characters:
1829
1830 #startElement: ShortDescription
1831 #characters: High quality matrices
1832 #endElement: ShortDescription
1833 #characters:
1834
1835 #startElement: Help
1836 #characters: When using a matrix with a cut-off which allows a false negative rate
1837 of 50%, the frequency of matches found in exon3 sequences (false positive rate)
1838 must drop below a certain threshold. This threshold is defined so that the
1839 matrices which produce the highest number of false positive matches are defined
1840 as low quality matrices (about 30% of the TRANSFAC matrices).
1841 #endElement: Help
1842 #characters:
1843
1844 #startElement: Value
1845 #characters: high
1846 #endElement: Value
1847 #characters:
1848
1849 #startElement: DefaultValue
1850 #characters: high
1851 #endElement: DefaultValue
1852 #characters:
1853
1854 #endElement: OptionalArgument
1855 #characters:
1856
1857
1858 #startElement: ListArgument
1859 #characters:
1860
1861 #startElement: ShortDescription
1862 #characters: If matrix: Matrix cut-off selection
1863 #endElement: ShortDescription
1864 #characters:
1865
1866 #startElement: Help
1867 #characters: For any group of matrices, you can specify the cut-offs for core and
1868 matrix similarity . The matrix similarity is a score that describes the
1869 quality of a match between a matrix and an arbitrary part of the input
1870 sequences. Analogously, the core similarity denotes the quality of a match
1871 between the core sequence of a matrix (i.e. the five most conserved positions
1872 within a matrix) and a part of the input sequence. A match has to contain
1873 the "core sequence " of a matrix, i.e. the core sequence has to match with
1874 a score higher than or equal to the core similarity cut-off. In addition,
1875 only those matches which score higher than or equal to the matrix similarity
1876 threshold appear in the output.
1877 #endElement: Help
1878 #characters:
1879
1880 #startElement: Value
1881 #characters: FP
1882 #endElement: Value
1883 #characters:
1884
1885 #startElement: PossibleValue
1886 #characters: FP
1887 #endElement: PossibleValue
1888 #characters:
1889
1890 #startElement: PossibleValue
1891 #characters: FN
1892 #endElement: PossibleValue
1893 #characters:
1894
1895 #startElement: PossibleValue
1896 #characters: SUM
1897 #endElement: PossibleValue
1898 #characters:
1899
1900 #startElement: PossibleValue
1901 #characters: SUM
1902 #endElement: PossibleValue
1903 #characters:
1904
1905 #startElement: DefaultValue
1906 #characters: FP
1907 #endElement: DefaultValue
1908 #characters:
1909
1910 #endElement: ListArgument
1911 #characters:
1912
1913
1914 #startElement: NumberArgument
1915 #characters:
1916
1917 #startElement: ShortDescription
1918 #characters: If "specify cut-offs": Matrix similarity
1919 #endElement: ShortDescription
1920 #characters:
1921
1922 #startElement: Help
1923 #characters: For any group of matrices, you can specify the cut-offs for core and
1924 matrix similarity . The matrix similarity is a score that describes the
1925 quality of a match between a matrix and an arbitrary part of the input
1926 sequences. Analogously, the core similarity denotes the quality of a match
1927 between the core sequence of a matrix (i.e. the five most conserved positions
1928 within a matrix) and a part of the input sequence. A match has to contain
1929 the "core sequence " of a matrix, i.e. the core sequence has to match with
1930 a score higher than or equal to the core similarity cut-off. In addition,
1931 only those matches which score higher than or equal to the matrix similarity
1932 threshold appear in the output.
1933 #endElement: Help
1934 #characters:
1935
1936 #startElement: Value
1937 #characters: 0.7
1938 #endElement: Value
1939 #characters:
1940
1941 #startElement: DefaultValue
1942 #characters: 0.7
1943 #endElement: DefaultValue
1944 #characters:
1945
1946 #endElement: NumberArgument
1947 #characters:
1948
1949
1950 #startElement: NumberArgument
1951 #characters:
1952
1953 #startElement: ShortDescription
1954 #characters: If "specify cut-offs": Matrix core siml.
1955 #endElement: ShortDescription
1956 #characters:
1957
1958 #startElement: Help
1959 #characters: For any group of matrices, you can specify the cut-offs for core and
1960 matrix similarity . The matrix similarity is a score that describes the
1961 quality of a match between a matrix and an arbitrary part of the input
1962 sequences. Analogously, the core similarity denotes the quality of a match
1963 between the core sequence of a matrix (i.e. the five most conserved positions
1964 within a matrix) and a part of the input sequence. A match has to contain
1965 the "core sequence " of a matrix, i.e. the core sequence has to match with
1966 a score higher than or equal to the core similarity cut-off. In addition,
1967 only those matches which score higher than or equal to the matrix similarity
1968 threshold appear in the output.
1969 #endElement: Help
1970 #characters:
1971
1972 #startElement: Value
1973 #characters: 0.75
1974 #endElement: Value
1975 #characters:
1976
1977 #startElement: DefaultValue
1978 #characters: 0.75
1979 #endElement: DefaultValue
1980 #characters:
1981
1982 #endElement: NumberArgument
1983 #characters:
1984
1985
1986 #startElement: ListArgument
1987 #characters:
1988
1989 #startElement: ShortDescription
1990 #characters: If Profiles: Group of profiles
1991 #endElement: ShortDescription
1992 #characters:
1993
1994 #startElement: Help
1995 #characters: We mainly provide tissue-specific profiles. Groups of transcription factors known to
1996 be active in a particular tissue have been collected for each profile with the
1997 help of information from the TRANSFAC® database. Matrices linked to these transcription
1998 factors in TRANSFAC® were then collected. When more than one matrix was linked to a
1999 transcription factor, we had to decide which matrix to include in the profile.
2000 We used the following criterion: If possible (i.e. if there was such a matrix) only
2001 matrices that fulfilled the "high quality criterion" were accepted. If several of the
2002 matrices fulfilling the criterion were linked to the same transcription factor, we
2003 estimated how many of the genomic binding sites of TRANSFAC® for this particular
2004 transcription factor could be recognized with each of these matrices. We include in
2005 the profile the matrix that has the lowest level of false positive matches in exon2
2006 and exon3 sequences when identifying 90% of the set of the genomic binding sites
2007 at the same time. The cut-offs used in the tissue specific profiles are those that
2008 minimize false negative matches. We also offer an additional profile called the
2009 "best selection profile". This profile has been constructed in the following way:
2010 TRANSFAC® contains several groups of matrices for the same transcription factor.
2011 We selected some of these groups and included just one matrix out of such a group
2012 in the" best selection profile". We used the criteria described above for the
2013 tissue-specific profiles to decide which matrix to use. We chose cut-offs to
2014 minimize false negative matches for this profile.
2015 #endElement: Help
2016 #characters:
2017
2018 #startElement: Value
2019 #characters: muscle_specific.prf
2020 #endElement: Value
2021 #characters:
2022
2023 #startElement: PossibleValue
2024 #characters: muscle_specific.prf
2025 #endElement: PossibleValue
2026 #characters:
2027
2028 #startElement: PossibleValue
2029 #characters: immune_cell_specific.prf
2030 #endElement: PossibleValue
2031 #characters:
2032
2033 #startElement: PossibleValue
2034 #characters: cell_cycle_specific.prf
2035 #endElement: PossibleValue
2036 #characters:
2037
2038 #startElement: PossibleValue
2039 #characters: liver_specific.prf
2040 #endElement: PossibleValue
2041 #characters:
2042
2043 #startElement: PossibleValue
2044 #characters: best_selection.prf
2045 #endElement: PossibleValue
2046 #characters:
2047
2048 #startElement: DefaultValue
2049 #characters: best_selection.prf
2050 #endElement: DefaultValue
2051 #characters:
2052
2053 #endElement: ListArgument
2054 #characters:
2055
2056
2057 #endElement: Arguments
2058 #characters:
2059
2060
2061 #startElement: Parsers
2062 unable to find FieldDescriptor for 'Parsers' in ClassDescriptor of algorithm-description - ignoring extra element.
2063 #characters:
2064
2065 #startElement: SiteParser
2066 #characters:
2067
2068 #startElement: Field
2069 #characters: AccessionNo
2070 #endElement: Field
2071 #characters:
2072
2073 #startElement: Field
2074 #characters: ProfileID
2075 #endElement: Field
2076 #characters:
2077
2078 #startElement: Field
2079 #characters: Start
2080 #endElement: Field
2081 #characters:
2082
2083 #startElement: Field
2084 #characters: Strand
2085 #endElement: Field
2086 #characters:
2087
2088 #startElement: Field
2089 #characters: Core_Score
2090 #endElement: Field
2091 #characters:
2092
2093 #startElement: Field
2094 #characters: Score
2095 #endElement: Field
2096 #characters:
2097
2098 #startElement: Field
2099 #characters: SiteSequence
2100 #endElement: Field
2101 #characters:
2102
2103 #endElement: SiteParser
2104 #characters:
2105
2106 #endElement: Parsers
2107 #characters:
2108
2109
2110 #endElement: AlgorithmDescription
2111 DEBUG [main] (AlgorithmVector.java:81) - Algorithm nullloaded
2112 INFO [main] (AlignedSequences.java:388) - Empty sequence database initialized.
2113 DEBUG [main] (MainFrame.java:212) - opening actions as inputstream
2114 DEBUG [main] (ActionManager.java:161) - Loading icon jar:file:/F:/max/jbproject/jannotatix/jannotatix.jar!/img/open.gif
2115 DEBUG [main] (ActionManager.java:161) - Loading icon jar:file:/F:/max/jbproject/jannotatix/jannotatix.jar!/img/open.gif
2116 ERROR [main] (ActionManager.java:166) - Could not find Icon null
2117 ERROR [main] (ActionManager.java:166) - Could not find Icon null
2118 ERROR [main] (ActionManager.java:166) - Could not find Icon null
2119 DEBUG [main] (ActionManager.java:161) - Loading icon jar:file:/F:/max/jbproject/jannotatix/jannotatix.jar!/img/Gearwheel.gif
2120 ERROR [main] (ActionManager.java:166) - Could not find Icon null
2121 ERROR [main] (ActionManager.java:166) - Could not find Icon null
2122 DEBUG [main] (ActionManager.java:161) - Loading icon jar:file:/F:/max/jbproject/jannotatix/jannotatix.jar!/img/find.gif
2123 ERROR [main] (ActionManager.java:166) - Could not find Icon null
2124 ERROR [main] (ActionManager.java:166) - Could not find Icon null
2125 ERROR [main] (ActionManager.java:166) - Could not find Icon null
2126 DEBUG [main] (ActionManager.java:161) - Loading icon jar:file:/F:/max/jbproject/jannotatix/jannotatix.jar!/img/save.gif
2127 DEBUG [main] (MainFrame.java:72) - trying to load F:\max\jbproject\jannotatix\testfiles\mpi-genes.fa and F:\max\jbproject\jannotatix\testfiles\standardtest.gff
2128 DEBUG [main] (AlignedSequences.java:95) - Loading, current dir is f:\max\jbproject\jannotatix
2129 INFO [main] (AlignedSequences.java:141) - Loading Sequence 1 successful.
2130 INFO [main] (AlignedSequences.java:141) - Loading Sequence 2 successful.
2131 INFO [main] (AlignedSequences.java:141) - Loading Sequence 3 successful.
2132 INFO [main] (AlignedSequences.java:141) - Loading Sequence 4 successful.
2133 INFO [main] (AlignedSequences.java:141) - Loading Sequence 5 successful.
2134 INFO [main] (AlignedSequences.java:141) - Loading Sequence 6 successful.
2135 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2136 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2137 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2138 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2139 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2140 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2141 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2142 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2143 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2144 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2145 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2146 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2147 INFO [main] (AlignedSequences.java:176) - Loading GFF-File F:\max\jbproject\jannotatix\testfiles\standardtest.gff
2148 INFO [main] (AlignedSequences.java:388) - Reading GFF...
2149 INFO [main] (AlignedSequences.java:388) - Adding features to sequences...
2150 DEBUG [main] (TrackedSequence.java:77) - create new track AlignAce
2151 DEBUG [main] (Track.java:117) - SetSource to AlignAce
2152 DEBUG [main] (TrackManager.java:108) - Tracktype created AlignAce
2153 DEBUG [main] (TrackedSequence.java:77) - create new track PLantcare Website
2154 DEBUG [main] (Track.java:117) - SetSource to PLantcare Website
2155 DEBUG [main] (TrackManager.java:108) - Tracktype created PLantcare Website
2156 DEBUG [main] (TrackedSequence.java:77) - create new track AlignAce
2157 DEBUG [main] (Track.java:117) - SetSource to AlignAce
2158 DEBUG [main] (TrackedSequence.java:77) - create new track PLantcare Website
2159 DEBUG [main] (Track.java:117) - SetSource to PLantcare Website
2160 DEBUG [main] (TrackedSequence.java:77) - create new track AlignAce
2161 DEBUG [main] (Track.java:117) - SetSource to AlignAce
2162 DEBUG [main] (TrackedSequence.java:77) - create new track PLantcare Website
2163 DEBUG [main] (Track.java:117) - SetSource to PLantcare Website
2164 DEBUG [main] (TrackedSequence.java:77) - create new track AlignAce
2165 DEBUG [main] (Track.java:117) - SetSource to AlignAce
2166 DEBUG [main] (TrackedSequence.java:77) - create new track PLantcare Website
2167 DEBUG [main] (Track.java:117) - SetSource to PLantcare Website
2168 DEBUG [main] (TrackedSequence.java:77) - create new track AlignAce
2169 DEBUG [main] (Track.java:117) - SetSource to AlignAce
2170 DEBUG [main] (TrackedSequence.java:77) - create new track PLantcare Website
2171 DEBUG [main] (Track.java:117) - SetSource to PLantcare Website
2172 DEBUG [main] (TrackedSequence.java:77) - create new track AlignAce
2173 DEBUG [main] (Track.java:117) - SetSource to AlignAce
2174 DEBUG [main] (TrackedSequence.java:77) - create new track PLantcare Website
2175 DEBUG [main] (Track.java:117) - SetSource to PLantcare Website
2176 INFO [main] (AlignedSequences.java:380) - Added 2888 features to 6 sequences
2177 INFO [main] (AlignedSequences.java:388) - Rebuilding alignments...
2178 INFO [main] (AlignedSequences.java:388) - Gff successfully imported.
2179 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack AlignAce
2180 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 0.0
2181 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack PLantcare Website
2182 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 9.0
2183 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2184 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack AlignAce
2185 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 0.0
2186 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack PLantcare Website
2187 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 9.0
2188 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2189 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack AlignAce
2190 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 0.0
2191 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack PLantcare Website
2192 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 9.0
2193 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2194 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack AlignAce
2195 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 0.0
2196 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack PLantcare Website
2197 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 9.0
2198 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2199 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack AlignAce
2200 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 0.0
2201 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack PLantcare Website
2202 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 9.0
2203 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2204 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack AlignAce
2205 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 0.0
2206 DEBUG [main] (SequenceViewer.java:154) - Drawing sourcetrack PLantcare Website
2207 DEBUG [main] (TrackViewer.java:142) - Repainting Track, displace is 9.0
2208 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2209 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2210 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2211 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2212 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2213 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2
2214 DEBUG [main] (SequenceViewer.java:103) - scale set to 7.2