Augustus的安装和使用参数
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
1. Augustus的安装
Augustus下载：http://bioinf.uni-greifswald.de/augustus/binaries/
$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.7.tar.gz $ tar zxf augustus.2.7.tar.gz $ cd augustus.2.7 $ cd src $ make -j 8 $ export AUGUSTUS_CONFIG_PATH=$PWD/../config/ (可以加入到.bashrc中）
2. Augustus使用方法
2.1 基因预测例子
$ augustus --strand=both --genemode=partial --singlestrand=false --hintsfile=hints.gff --extrinsicCfgFile=extrinsic.cfg --protein=on --introns=on --start=on --stop=on --cds=on --codingseq=on --alternatives-from-evidence=true --gff3=on --UTR=on ----outfile=out.gff --species=human genome.fa $ augustus --noprediction=true --species=SPECIES sequences.gb
2.2 Augustus使用参数
Usage:
augustus [parameters] --sepcies=SPECIES queryfilename
重要参数：
--strand=both, --strand=forward or --strand=backward report predicted genes on both strands, just the forward or just the backward strand.default is 'both' --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 (ex trinsic information) is turned on. hintsfilename contains the hints in gff format. --extrinsicCfgFile=cfgfilename Optional. This file contains the list of used sources for the hints and their boni and mali. If not specified the file "extrin sic.cfg" in the config directory $AUGUSTUS_CONFIG_PATH is used. --maxDNAPieceSize=n This value specifies the maximal length of the pieces that the sequence is cut into for the core algorithm (Viterbi) to be run. Default is --maxDNAPieceSize=200000. AUGUSTUS tries to place the boundaries of these pieces in the intergenic region, which is inferred by a preliminary prediction. GC-content dependent parameters are chosen for each piece of DNA if /Constant/decomp_num_steps > 1 for that species. This is why this value should not be set very large, even if you have plenty of memory. --protein=on/off --introns=on/off --start=on/off --stop=on/off --cds=on/off --codingseq=on/off Output options. Output predicted protein sequence, introns, start codons, stop codons. Or use 'cds' in addition to 'initial', 'internal', 'terminal' and 'single' exon. The CDS excludes the stop codon (unless stopCodonExcludedFromCDS=false) whereas the terminal and single exon include the stop codon. --AUGUSTUS_CONFIG_PATH=path path to config directory (if not specified as environment var iable) --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 --proteinprofile=filename Read a protein profile from file filename. See section 7 below. --predictionStart=A, --predictionEnd=B A and B define the range of the sequence for which predictions should be found. Quicker if you need predictions only for a small part. --gff3=on/off output in gff3 format. --UTR=on/off predict the untranslated regions in addition to the coding sequence. This currently works only for human, galdieria, toxopl asma and caenorhabditis. --outfile=filename print output to filename instead to standard output. This is useful for computing environments, e.g. parasol jobs, which do not allow shell redirection. --noInFrameStop=true/false Don't 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. Augustus也可以以 genebank格式文件为输入文件，进行基因预测，并将预测结果和genebank的结果进行比较后 得出一个精确性的统计结果。 当然，由于genebank格式文件中有些sequences没有cds的注释结果，因此可以使用该 参数进行检测，从而得到没有cds的序列号，在人为去去除这些没有cds注释的序列，再去进行 预测准确性的评估。 --contentmodels=on/off If 'off' the content models are disabled (all emissions unif ormly 1/4). The content models are; coding region Markov chain (emiprobs), initial k-mers in coding region (Pls), intron and int ergenic regin Markov chain. This option is intended for special applications that require judging gene structures from the signal models only, e.g. for predicting the effect of SNPs or mutations on splicing. For all typical gene predictions, this should be true. Default: on --paramlist For a complete list of parameters, type "augustus --paramlist"
转载自：http://sihua.us/Augustus.htm