基因预测总结.pdfVIP

1、基因预测 对于真菌来说有四个ab initio 预测软件： GlimmerHMM，SNAP，Genearkes,augustus 以及同源预测 （homology）。四个 软件中：GeneMarkes 是通过隐马模型工作的，但是它不需要参考物种，是自身 训练的，不需要参考序列，当处理一个新物种，没有理想的或者较近缘的已测序 物种时可以采用这种方法。Augustus，GlimmerHMM，SNAP 都需要参考训练集的。 总流程： perl /nas/MG01/FUNGUS/PGAP/FGAP.pl [options] Genome.fa Options --all run all analysis for Fungi --cutlen int cut the scaffolds longer than this --predict str select the method to predict genes: augustus,genemarkes,snap,glimmerhmm or homology --prepara str set the parament for augustus,snap,homology --repeat str set repeat method, defalut: repbase-proteinmasker-trf --ncRNA str set ncRNA type, default: tRNA-rRNA-miRNA-sRNA-snRNA --rRNA_ref file set Reference for rRNA, if null rRNA will be predicted by rRNAmmer --function str set dbs for gene function annotaion,default: nr-swissprot-trembl-cog-kegg-iprscan --lib file set the lib for synteny analysis and gene family analysis, needed --synteny synteny analysis --family Gene Family analysi --species file species tree, default, created by lib information --category file category file, default, created by lib information --cpu int set the cpu number to use in parallel, default 20 for qsub and 5 for multi --run str set the parallel type, qsub, or multi, default=qsub --outdir str set the result directory, default=. --prefix str set a prefix name for results --help output help information to screen 分步流程程序路径： /nas/MG01/FUNGUS/PGAP/gene-prediction/bin/gene-predict.pl perl gene-predict.pl [options] seq.file --glimmer run glimmer by self training --genemark run genemark by self training --shape str set the shape of prokaryote DNA, circular,linear,par