gth1

Usage

Overview

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