Provided by: genomethreader_1.7.3+dfsg-5_amd64 
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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