# gth(1)

## 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
