$ GenomeThreader 0.9.38 (2005-06-24 17:37:20) $ Date run: 2005-08-10 20:36:46 $ Splice Site Model: Bayesian $ $ genomicfile = "OSchr10" $ referencefile = "LIBc9" $ species = "rice" $ proteinsmap = "protein" $ scorematrix = "BLOSUM62" $ bssmfile = "rice" $ searchmode = (forward=True,reverse=True) $ frompos = 1 (non-df.) $ topos = 600000 (non-df.) $ width = 0 (default) $ verbose = False (default) $ gs2out = False (default) $ showintronmaxlen = 120 (default) maximum length of a fully shown intron $ minorflen = 64 (default) minimum length of an ORF to be shown $ minmatchlen = 45 (non-df.) minimum match length $ seedlength = 30 (non-df.) the seed length $ exdrop = 2 (default) the xdrop value for edit distance $ online = False (default) run the similarity filter online $ inverse = True (non-df.) invert query and index in vmatch call $ exact = False (default) use exact matches $ noautoindex = False (default) do not create indices automatically $ maskpolyatails = True (non-df.) mask poly(A) tails in cDNA/EST files $ maxnumofmatches = 0 (default) maximum number of matches $ matchnumdistri = False (default) show the distribution of matches $ chainlocal = 1 (default) local chains (according to L1-model). $ uselocalchaining = False (default) enable local chaining $ chainwf = 0.500000 (default) weight factor > 0.0 for local chaining $ gcmaxgapwidth = 50000 (non-df.) maximum gap width for global chains $ gcmincoverage = 15 (non-df.) minimum coverage of global chains $ introncutout = False (default) enable the intron cutout technique $ autointroncutout = 0 (default) automatic intron cutout matrix size $ icinitialdelta = 50 (default) initial delta used for intron cutouts $ iciterations = 2 (default) number of intron cutout iterations $ icdeltaincrease = 50 (default) delta increase during every iteration $ icminremintronlen= 10 (default) minimum remaining intron length $ nou12intronmodel = False (default) disable the U12-type intron model $ u12donorprob = 0.990000 (default) probability for perfect U12-type donor $ u12donorprob1mism= 0.900000 (default) prob. for U12-type donor w. 1 mismatch $ probies = 0.500000 (default) initial exon state probability $ probdelgen = 0.030000 (default) genomic sequence deletion probability $ identityweight = 2.000000 (default) pairs of identical characters weight $ mismatchweight = -2.000000 (default) weight for mismatching characters $ undetcharweight = 0.000000 (default) weight for undetermined characters $ deletionweight = -5.000000 (non-df.) weight for deletions $ dpminexonlen = 5 (default) minimum exon length for the DP $ dpminintronlen = 50 (default) minimum intron length for the DP $ shortexonpenal = 100 (default) short exon penalty $ shortintronpenal = 100 (default) short intron penalty $ wzerotransition = 80 (default) zero transition weights window size $ wdecreasedoutput = 80 (default) decreased output weights window size $ leadcutoffsmode = RELAXED (default) cutoffs mode for leading bases $ termcutoffsmode = STRICT (default) cutoffs mode for terminal bases $ cutoffsminexonlen= 5 (default) cutoffs minimum exon length $ scoreminexonlen = 50 (default) score minimum exon length $ minaveragessp = 0.500000 (default) minimum average splice site prob. $ intermediate = False (default) stop after calc. of spliced alignments $ sortags = False (default) sort alternative gene structures $ sortagswf = 1.000000 (default) weight factor for the sorting of AGSs $ first = 0 (default) maximum number of spliced alignments $ $ special output characters for starting lines: $ GTHINFOCHAR = $ (info line) $ VMATCHCHAR = # (mkvtree and vmatch output) $ $ the specified BSSM parameter file contains the following models: $ GT donor sites = True $ GC donor sites = True $ AG acceptor sites= True $