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amber进行MD的步骤如下：PDB文件需要去掉结晶水、氢 和金属离子（非必须）。 网上教程：http://enzyme.fbb.msu.ru/Tutorials/ 金属酶的模拟：http://ambermd.org/tutorials/advanced/tutorial1_orig/ 蛋白和配体的模拟： 1：分子系统的准备 命令如下： tleap //进入leap source leaprc.ff99SB //加载蛋白力场 source leaprc.gaff //如果有小分子加载小[……] […] > library(caTools); > library(bitops); > library(grid); > data=read.csv(“/home/shenzy/Desktop/R/Bac.heatmap1.csv”) > data=read.csv(“/home/shenzy/Desktop/R/Bac.heatmap1.2.csv”) > View(data) > data=read.csv(“/home/shenzy/Desktop/R/Bac.heatmap1.2.csv”,sep=”\t”) > View(dat[……] […]
NCBI 有时批量下载的protein sequence会有不一致时，可以从以下资源数据库下载（eg, eth195) http://cmr.jcvi.org/cgi-bin/CMR/shared/MakeFrontPages.cgi?page=batchdownload […] Circos: nucmer –prefix=refBAV1_qryVScds Dehalococcoides_BAV1.fasta Dehalococcoides_VS.cds.fasta show-tiling -i 80 -c refBAV1_qryVScds.delta > refBAV1_qryVScds.tiling awk -F ” ” ‘{print “chr1″ “\t” $1 “\t” $2}’ refBAV1_qryVScds.tiling > Dehalococcoidessp.VScds.gene_tableBAV1.txt shenzy@s[……] […] Codon adaptation index (CAI) is one of them. To examine the CAI value of a gene, a reference table of RSCU (relative synonymous codon usage) values for highly expressed genes is compiled. A software call CodonW, you can download it from: http://codonw.sourceforge.net/. There is also a PhD thesis[……] […] ############################### PCA ############################### install.packages(“vegan”) library(vegan) > STpcoa<-read.table(file=”bactera_16s_final.subsample.phylip.tre1.weighted.phylip.pcoa.axes”, header=T,row.names=1) > STpcoa axis1 axis2 axis3 axis4 Cellulose -0.020878[……] […] Difference between prcomp and princomp: ‘princomp’ can only be used with more units than variables” prcomp是基于SVD分解（svd()函数，princomp是基于特征向量eigen()函数) Good video source: http://www.youtube.com/watch?v=oZ2nfIPdvjY http://www.youtube.com/watch?v=I5GxNzKLIoU&feature=relmfu http://ww[……] […] > gtsdata_test=read.table(“gtsdata.txt”, header=T) > gtsenv=read.table(“gtsenv.txt”, header=T) > gtsdata_data_t<-t(gtsdata_data) > decorana(gtsdata_data_t) Call: decorana(veg = gtsdata_data_t) Detrended correspondence analysis with 26 segments. Rescaling of axes w[……] […] “基于Vegan 软件包的生态学数据排序分析 赖江山 米湘成 (中国科学院植物研究所植被与环境变化国家重点实验室，北京 100093) 摘要：群落学数据一般是多维数据，例如物种属性或环境因子的属性。多元统计分析是群落生态学常用的分析方法，排序（ordination）是多元统计最常用的方法之一。CANOCO是广泛使用的排序软件，但缺点是商业软件价格不菲，版本更新速度也很慢。近年来，R语言以其灵活、开放、易于掌握、免费等诸多优点，在生态学和生物多样性研究领域迅速赢得广大研究人员的青睐。R语言中的外在软件包“Vegan”是专门用于群落生态学分析的工具。Vegan能够提供所有基本的排序方法，同时[……] […] |
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