Provided by: genomethreader_1.7.3+dfsg-10build2_amd64 bug

NAME

       gth - predict genome structures

SYNOPSIS

       gth [option ...] -genomic file [...] -cdna file [...] -protein file [...]

DESCRIPTION

       Computes similarity-based gene structure predictions (spliced alignments) using cDNA/EST
       and/or protein sequences and assemble the resulting spliced alignments to consensus
       spliced alignments.

OPTIONS

       -genomic <file>
           specify input files containing genomic sequences (mandatory option)

       -cdna <file>
           specify input files containing cDNA/EST sequences

       -protein <file>
           specify input files containing protein sequences

       -species <species>
           specify species to select splice site model which is most appropriate; possible
           species: "human" "mouse" "rat" "chicken" "drosophila" "nematode" "fission_yeast"
           "aspergillus" "arabidopsis" "maize" "rice" "medicago" default: undefined

       -bssm
           read bssm parameter from file in the path given by the environment variable BSSMDIR,
           default: undefined

       -scorematrix
           read amino acid substitution scoring matrix from file in the path given by the
           environment variable GTHDATADIR default: BLOSUM62

       -translationtable
           set the codon translation table used for codon translation in matching, DP, and output
           default: 1

       -f
           analyze only forward strand of genomic sequences default: no

       -r
           analyze only reverse strand of genomic sequences default: no

       -cdnaforward
           align only forward strand of cDNAs default: no

       -frompos
           analyze genomic sequence from this position requires -topos or -width; counting from 1
           on default: 0

       -topos
           analyze genomic sequence to this position requires -frompos; counting from 1 on
           default: 0

       -width
           analyze only this width of genomic sequence requires -frompos default: 0

       -v
           be verbose default: no

       -xmlout
           show output in XML format default: no

       -gff3out
           show output in GFF3 format default: no

       -md5ids
           show MD5 fingerprints as sequence IDs default: no

       -o
           redirect output to specified file default: undefined

       -gzip
           write gzip compressed output file default: no

       -bzip2
           write bzip2 compressed output file default: no

       -force
           force writing to output file default: no

       -skipalignmentout
           skip output of spliced alignments default: no

       -mincutoffs
           show full spliced alignments i.e., cutoffs mode for leading and terminal bases is
           MINIMAL default: no

       -showintronmaxlen
           set the maximum length of a fully shown intron If set to 0, all introns are shown
           completely default: 120

       -minorflen
           set the minimum length of an ORF to be shown default: 64

       -startcodon
           require than an ORF must begin with a start codon default: no

       -finalstopcodon
           require that the final ORF must end with a stop codon default: no

       -showseqnums
           show sequence numbers in output default: no

       -pglgentemplate
           show genomic template in PGL lines (switch off for backward compatibility) default:
           yes

       -gs2out
           output in old GeneSeqer2 format default: no

       -maskpolyatails
           mask poly(A) tails in cDNA/EST files default: no

       -proteinsmap
           specify smap file used for protein files default: protein

       -noautoindex
           do not create indices automatically except for the .dna.* files used for the DP.
           existence is not tested before an index is actually used! default: no

       -createindicesonly
           stop program flow after the indices have been created default: no

       -skipindexcheck
           skip index check (in preprocessing phase) default: no

       -minmatchlen
           specify minimum match length (cDNA matching) default: 20

       -seedlength
           specify the seed length (cDNA matching) default: 18

       -exdrop
           specify the Xdrop value for edit distance extension (cDNA matching) default: 2

       -prminmatchlen
           specify minimum match length (protein matches) default: 24

       -prseedlength
           specify seed length (protein matching) default: 10

       -prhdist
           specify Hamming distance (protein matching) default: 4

       -online
           run the similarity filter online without using the complete index (increases runtime)
           default: no

       -inverse
           invert query and index in vmatch call default: no

       -exact
           use exact matches in the similarity filter default: no

       -gcmaxgapwidth
           set the maximum gap width for global chains defines approximately the maximum intron
           length set to 0 to allow for unlimited length in order to avoid false-positive exons
           (lonely exons) at the sequence ends, it is very important to set this parameter
           appropriately! default: 1000000

       -gcmincoverage
           set the minimum coverage of global chains regarding to the reference sequence default:
           50

       -paralogs
           compute paralogous genes (different chaining procedure) default: no

       -enrichchains
           enrich genomic sequence part of global chains with additional matches default: no

       -introncutout
           enable the intron cutout technique default: no

       -fastdp
           use jump table to increase speed of DP calculation default: no

       -autointroncutout
           set the automatic intron cutout matrix size in megabytes and enable the automatic
           intron cutout technique default: 0

       -icinitialdelta
           set the initial delta used for intron cutouts default: 50

       -iciterations
           set the number of intron cutout iterations default: 2

       -icdeltaincrease
           set the delta increase during every iteration default: 50

       -icminremintronlen
           set the minimum remaining intron length for an intron to be cut out default: 10

       -nou12intronmodel
           disable the U12-type intron model default: no

       -u12donorprob
           set the probability for perfect U12-type donor sites default: 0.99

       -u12donorprob1mism
           set the prob. for U12-type donor w. 1 mismatch default: 0.90

       -probies
           set the initial exon state probability default: 0.50

       -probdelgen
           set the genomic sequence deletion probability default: 0.03

       -identityweight
           set the pairs of identical characters weight default: 2.00

       -mismatchweight
           set the weight for mismatching characters default: -2.00

       -undetcharweight
           set the weight for undetermined characters default: 0.00

       -deletionweight
           set the weight for deletions default: -5.00

       -dpminexonlen
           set the minimum exon length for the DP default: 5

       -dpminintronlen
           set the minimum intron length for the DP default: 50

       -shortexonpenal
           set the short exon penalty default: 100.00

       -shortintronpenal
           set the short intron penalty default: 100.00

       -wzerotransition
           set the zero transition weights window size default: 80

       -wdecreasedoutput
           set the decreased output weights window size default: 80

       -leadcutoffsmode
           set the cutoffs mode for leading bases can be either RELAXED, STRICT, or MINIMAL
           default: RELAXED

       -termcutoffsmode
           set the cutoffs mode for terminal bases can be either RELAXED, STRICT, or MINIMAL
           default: STRICT

       -cutoffsminexonlen
           set the cutoffs minimum exon length default: 5

       -scoreminexonlen
           set the score minimum exon length default: 50

       -minaveragessp
           set the minimum average splice site prob. default: 0.50

       -duplicatecheck
           criterion used to check for spliced alignment duplicates, choose from
           none|id|desc|seq|both default: both

       -minalignmentscore
           set the minimum alignment score for spliced alignments to be included into the set of
           spliced alignments default: 0.00

       -maxalignmentscore
           set the maximum alignment score for spliced alignments to be included into the set of
           spliced alignments default: 1.00

       -mincoverage
           set the minimum coverage for spliced alignments to be included into the set of spliced
           alignments default: 0.00

       -maxcoverage
           set the maximum coverage for spliced alignments to be included into the set of spliced
           alignments default: 9999.99

       -intermediate
           stop after calculation of spliced alignments and output results in reusable XML
           format. Do not process this output yourself, use the ``normal'' XML output instead!
           default: no

       -sortags
           sort alternative gene structures according to the weighted mean of the average exon
           score and the average splice site probability default: no

       -sortagswf
           set the weight factor for the sorting of AGSs default: 1.00

       -exondistri
           show the exon length distribution default: no

       -introndistri
           show the intron length distribution default: no

       -refseqcovdistri
           show the reference sequence coverage distribution default: no

       -first
           set the maximum number of spliced alignments per genomic DNA input. Set to 0 for
           unlimited number. default: 0

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

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