---
name: "gth"
section: "1"
platform: "linux"
package: "genomethreader"
version: "1.7.3+dfsg-10+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gth"
---

# gth(1)

predict genome structures

## 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