Month: July 2020
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PHAST安装使用
PHAST：Phylogenetic Analysis with Space/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling,…
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使用MCScanX和JCVI共线性区块分析
首先从基因组数据库下载目标物种的全基因组文件和gff3文件 对gff3文件预处理得到对应格式的gff和bed文件 MCScanX：perl -e ‘while () { if (m/^(\S+)\t.*\tgene\t(\d+)\t(\d+).*ID=(darer\d+)/) { print “$1\t$4\t$2\t$3\n” } }’ darer.genome.gff3 > darer.gff jcvi：perl -e ‘while () { if (m/^(\S+)\t.*\tgene\t(\d+)\t(\d+)\t(\S+)\t(\S+).*ID=(darer\d+)/) { print “$1\t$2\t$3\t$6\t$4\t$5\n” } }’ darer.genome.gff3 > zebr.bed 对NCBI的GFF3文件再进行提取，若基因含有可变剪接，则仅保留CDS长度最长的转录本并获得蛋白序列，该过程参考网上其他教程 cat darer.gff gc.gff > all.gff cat darer.pep.fasta gc.pep.fasta > all.pep.fasta makeblastdb -in all.pep.fasta -dbtype prot -title all -parse_seqids -out all -logfile all.log…