加载中…加载中…加载中…加载中…加载中…第一个：http://genome.jgi-psf.org/
MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison.
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杂谈 |
下载地址http://bio-bwa.sourceforge.net/bwa.shtml
第一步: 建立 Index
根据reference genome
data(e.g. reference.fa) 建立 Index File
[root@localhost ]# bwa index -a bwtsw human_hg18_ref.fa（human参考基因组18）
第二步: 寻找 SA coordinates
如果是pair-end 数据（leftRead.fastq和rightRead.fastq）两个文件分别处理
Genome-wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of hundreds of diseases. However, there is currently no database that enables non-specialists to answer the following simple questions: which SNPs associated with diseases are in linkage disequilibrium (LD) with a gene of interest? Which chromosomal regions have been associated with a given disease, and which are the potentially causal genes in each region? To answer these questions, we use data from the HapMap Project to partition each chromosome into so-called LD blocks, so that SNPs in LD with each other are preferentially in the same block, whereas SNPs not
> library(VennDiagram)
Loading required package: grid
Warning message:
package 'VennDiagram' was built under R version 2.13.0
> x <-
c(1,3,5,7,9,11,17,19,21,23,25,29,31,33,37,39,41,47,49,51,57,59)
> y <-
c(1,3,5,7,13,17,19,21,23,25,27,29,31,33,45,47,51)
> z <-
c(1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,55,57,59,61)
>
venn.diagram(list(X=x,Y=y,Z=z),fill=c('red','blue','yellow'),'out.tiff')
[1] 1
输出1表示画图成功，生成的结果是out.tiff，这个文件在你的R工作目录下。
另外附一个在线画Venn图的网站：
Special Issue Title: GWAS in complex human disease and traits
http://bfg.oxfordjournals.org/content/10/2.toc
PLoS Genetics（PLoS遗传学期刊）
I submit the accompanying manuscript entitled “Gain and loss of multiple genes during the evolution of Helicobacter pylori” by H. Gressmann et al. for publication in PLoS Genetics.
This manuscript presents the global variability within H. pylori in terms of presence or absence of almost all the genes within the two currently available genome sequences. The strains tested are representative of the global genetic diversity within H. pylori and also represent the diverse populations that exist in that organism. Global analyses of genomic content are very rare indeed for bacterial species and are new for H. pylori. By including isolates from the most closely related species, H.
找了1篇关于Fisher's Exact Test的文献
http://mathworld.wolfram.com/FishersExactTest.html
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Fisher's exact test is a statistical test used to determine if there are nonrandom associations between two categorical variables. Let there exist two such variables |
Ivona Aksentijevich & Daniel L. Kastner
p469 | doi:10.1038/nrrheum.2011.94
Advances in genetic research and technology have provided great insights into the pathogenesis of inherited diseases of the innate immune system. In this article, the authors review the contributions of genetic studies to the understanding of the mechanisms underlying these autoinflammatory
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