GenomeThreader 2016

Introduction

GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. GenomeThreader was motivated by disabling limitations in GeneSeqer, a popular gene prediction program which is widely used for plant genome annotation. [ https://genomethreader.org ¹]

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

• GenomeThreader/1.7.1-Linux_x86_64-64bit
• GenomeThreader/1.7.3-Linux_x86_64-64bit

Loading GenomeThreader

To load the desired version of the module, use the module load command, e.g.

module load hpc-env/8.3
module load GenomeThreader

Always remember: this commands are case sensitive!

Using GenomeThreader

To find out on how to use GenomeThreader you can just type in gth --help after loading the module to print out a help text to get you started:

$ gth --help
Usage: gth [option ...] -genomic file [...] -cdna file [...] -protein file [...]
Compute similarity-based gene structure predictions (spliced alignments)
using cDNA/EST and/or protein sequences and assemble the resulting spliced
alignments to consensus spliced alignments.

-genomic          specify input files containing genomic sequences
                  mandatory option
-cdna             specify input files containing cDNA/EST sequences
-protein          specify input files containing protein sequences
-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
-gs2out           output in old GeneSeqer2 format
                  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
-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
-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
-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
-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

For detailed information, please refer to the manual of GenomeThreader.
Report bugs to <gordon@gremme.org>.

Documentation

The full documentation can be found here.