[BioTools] Augustus

http://bioinf.uni-greifswald.de/augustus/

# wget http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/augustus-3.0.3.tar.gz

# tar zxvfp augustus-3.0.3.tar.gz

# cd augustus-3.0.3/

# make all

# /BiO/apps/augustus-3.0.3/bin/augustus

AUGUSTUS (3.0.3) is a gene prediction tool for eukaryotes

written by Mario Stanke (mstanke@gwdg.de) and Oliver Keller (keller@cs.uni-goettingen.de).

usage:

augustus [parameters] --species=SPECIES queryfilename

'queryfilename' is the filename (including relative path) to the file containing the query sequence(s)

in fasta format.

SPECIES is an identifier for the species. Use --species=help to see a list.

parameters:

--strand=both, --strand=forward or --strand=backward

--genemodel=partial, --genemodel=intronless, --genemodel=complete, --genemodel=atleastone or --genemodel=exactlyone

  partial      : allow prediction of incomplete genes at the sequence boundaries (default)

  intronless   : only predict single-exon genes like in prokaryotes and some eukaryotes

  complete     : only predict complete genes

  atleastone   : predict at least one complete gene

  exactlyone   : predict exactly one complete gene

--singlestrand=true

  predict genes independently on each strand, allow overlapping genes on opposite strands

  This option is turned off by default.

--hintsfile=hintsfilename

  When this option is used the prediction considering hints (extrinsic information) is turned on.

  hintsfilename contains the hints in gff format.

--AUGUSTUS_CONFIG_PATH=path

  path to config directory (if not specified as environment variable)

--alternatives-from-evidence=true/false

  report alternative transcripts when they are suggested by hints

--alternatives-from-sampling=true/false

  report alternative transcripts generated through probabilistic sampling

--sample=n

--minexonintronprob=p

--minmeanexonintronprob=p

--maxtracks=n

  For a description of these parameters see section 4 of README.TXT.

--proteinprofile=filename

  When this option is used the prediction will consider the protein profile provided as parameter.

  The protein profile extension is described in section 7 of README.TXT.

--progress=true

  show a progressmeter

--gff3=on/off

  output in gff3 format

--predictionStart=A, --predictionEnd=B

  A and B define the range of the sequence for which predictions should be found.

--UTR=on/off

  predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.

--noInFrameStop=true/false

  Do not report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur. Default: false

--noprediction=true/false

  If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.

--uniqueGeneId=true/false

  If true, output gene identifyers like this: seqname.gN

For a complete list of parameters, type "augustus --paramlist".

An exhaustive description can be found in the file README.TXT.