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\begin{supertabular}{ll}\hline
\Showoptiongroup{Input~Options}
\Showoption{genomic}& specify input files containing genomic sequences
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\Showoption{cdna}& specify input files containing cDNA/EST sequences
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\Showoption{protein}& specify input files containing protein sequences
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\Showoptiongroup{Parameter~Files}
\Showoption{species}& specify species to select splice site model
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\Showoption{bssm}& read bssm parameter from file
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\Showoption{scorematrix}& read amino acid substitution scoring matrix from file
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\Showoption{translationtable}& set the codon translation table
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\Showoptiongroup{Strand~Direction}
\Showoption{f}& analyze only forward strand of genomic sequences
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\Showoption{r}& analyze only reverse strand of genomic sequences
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\Showoption{cdnaforward}& align only forward strand of cDNAs
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\Showoptiongroup{Genomic~Sequence~Positions}
\Showoption{frompos}& analyze genomic sequence from this position
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\Showoption{topos}& analyze genomic sequence to this position
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\Showoption{width}& analyze only this width of genomic sequence
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\Showoptiongroup{Output}
\Showoption{v}& be verbose
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\Showoption{xmlout}& show output in XML format
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\Showoption{gff3out}& show output in GFF3 format
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\Showoption{md5ids}& show MD5 fingerprints as sequence IDs
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\Showoption{o}& redirect output to specified file
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\Showoption{gzip}& gzip compressed output file
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\Showoption{bzip2}& bzip2 compressed output file
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\Showoption{force}& force writing to output file
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\Showoption{skipalignmentout}& skip output of spliced alignments
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\Showoption{mincutoffs}& show full spliced alignments
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\Showoption{showintronmaxlen}& set the maximum length of a fully shown intron
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\Showoption{minorflen}& set the minimum length of an ORF to be shown
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\Showoption{startcodon}& require than an ORF must begin with a start codon
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\Showoption{finalstopcodon}& require that the final ORF must end with a stop codon
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\Showoption{showseqnums}& show sequence numbers in output
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\Showoption{pglgentemplate}& show genomic template in PGL lines
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\Showoption{gs2out}& output in old GeneSeqer2 format
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\Showoptiongroup{Data Preprocessing}
\Showoption{maskpolyatails}& mask poly(A) tails in cDNA/EST files
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\Showoption{proteinsmap}& specify smap file used for protein files
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\Showoption{noautoindex}& do not create indices automatically
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\Showoption{createindicesonly}& stop program flow after the indices have been created
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\Showoption{skipindexcheck}& skip index check (in preprocessing phase)
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\Showoptiongroup{Similarity~Filter}
\Showoption{minmatchlen}& specify minimum match length (cDNA matching)
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\Showoption{seedlength}& specify the seed length (cDNA matching)
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\Showoption{exdrop}& specify the Xdrop value for edit distance
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\Showoption{prminmatchlen}& specify minimum match length (protein matches)
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\Showoption{prseedlength}& specify seed length (protein matching)
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\Showoption{prhdist}& specify Hamming distance (protein matching)
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\Showoption{online}& run the similarity filter online
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\Showoption{inverse}& invert query and index in vmatch call
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\Showoption{exact}& use exact matches
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\Showoption{gcmaxgapwidth}& set the maximum gap width for global chains
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\Showoption{gcmincoverage}& set the minimum coverage of global chains
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\Showoption{paralogs}& compute paralogous genes (different chaining procedure)
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\Showoption{enrichchains}& enrich genomic sequence part of global chains with additional matches
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\Showoptiongroup{Intron~Cutout~Technique}
\Showoption{introncutout}& enable the intron cutout technique
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\Showoption{fastdp}& use jump table to increase speed of DP calculation
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\Showoption{autointroncutout}& set the automatic intron cutout matrix size
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\Showoption{icinitialdelta}& set the initial delta used for intron cutouts
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\Showoption{iciterations}& set the number of intron cutout iterations
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\Showoption{icdeltaincrease}& set the delta increase during every iteration
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\Showoption{icminremintronlen}& set the minimum remaining intron length
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\Showoptiongroup{U12-type~Intron~Model}
\Showoption{nou12intronmodel}& disable the U12-type intron model
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\Showoption{u12donorprob}& set the probability for perfect U12-type donor
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\Showoption{u12donorprob1mism}& set the prob. for U12-type donor w. 1 mismatch
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\Showoptiongroup{Basic~DP~Algorithm}
\Showoption{probies}& set the initial exon state probability
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\Showoption{probdelgen}& set the genomic sequence deletion probability
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\Showoption{identityweight}& set the pairs of identical characters weight
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\Showoption{mismatchweight}& set the weight for mismatching characters
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\Showoption{undetcharweight}& set the weight for undetermined characters
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\Showoption{deletionweight}& set the weight for deletions
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\Showoptiongroup{Short~Exon/Intron~Parameters}
\Showoption{dpminexonlen}& set the minimum exon length for the DP
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\Showoption{dpminintronlen}& set the minimum intron length for the DP
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\Showoption{shortexonpenal}& set the short exon penalty
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\Showoption{shortintronpenal}& set the short intron penalty
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\Showoptiongroup{Special~Parameters~DP~Algorithm}
\Showoption{wzerotransition}& set the zero transition weights window size
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\Showoption{wdecreasedoutput}& set the decreased output weights window size
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\Showoptiongroup{Processing of ``raw'' spliced alignments}
\Showoption{leadcutoffsmode}& set the cutoffs mode for leading bases
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\Showoption{termcutoffsmode}& set the cutoffs mode for terminal bases
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\Showoption{cutoffsminexonlen}& set the cutoffs minimum exon length
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\Showoption{scoreminexonlen}& set the score minimum exon length
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\Showoptiongroup{Advanced~Similarity~Filter~Option}
\Showoption{minaveragessp}& set the minimum average splice site prob.
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\Showoptiongroup{Spliced~Alignment~Filter}
\Showoption{minalignmentscore}& set the minimum alignment score
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\Showoption{maxalignmentscore}& set the maximum alignment score
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\Showoption{mincoverage}& set the minimum coverage
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\Showoption{maxcoverage}& set the maximum coverage
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\Showoption{intermediate}& stop after calc. of spliced alignments
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\Showoption{sortags}& sort alternative gene structures
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\Showoption{sortagswf}& set the weight factor for the sorting of AGSs
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\Showoption{exondistri}& show the exon length distribution
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\Showoption{introndistri}& show the intron length distribution
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\Showoption{refseqcovdistri}& show the reference sequence coverage distribution
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\Showoption{first}& set the maximum number of spliced alignments
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\Showoption{help}& show basic options and exit
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\Showoption{help+}& show all options and exit
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\Showoption{version}& display version information and exit
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\hline
\end{supertabular}
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