BEReX : Biomedical Entity-Relation eXplorer

 BEReX is a new biomedical knowledge integration, search, and exploration tool. BEReX integrates eight popular databases (STRING, DrugBank, KEGG, PharmGKB, BioGRID, GO, HPRD, and MSigDB) and delineates an integrated network by combining the information available from these databases. Users search th[……]

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multiple sequence alignment software

PAGAN is a general-purpose method for the alignment of sequence graphs. It includes e.g.:

  • phylogenetic multiple sequence alignment
  • alignment extension by phylogenetic sequence placement
  • modelling of Roche 454 sequencing error
  • alignment and placement of NGS sequences
  • pileup alignment of s[……]

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awk 一些简单的用法

# 打印每行,并删除第二列

  • awk ‘{ $2 = “”; print }’ file1
  • awk ‘{ $2 = “”;$1 = “”; print }’ test1
# 打印部分文本
bash-3.2$ # 打印文件的前十行 (模拟 “head”)   bash-3.2$ awk ‘NR < 11′ test1     # 打印文件的最后两行 (模拟 “tail -2″awk ‘{y=x “\n” $0; x=$0};END{print y}’   # 打印文件的最后[……]

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Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes.

 

Description

 

Cake is a bioinformatics tool to identify putative somatic mutations from cancer genome/exome data. Cake combines somatic calls from a number of publicly available SNP/somatic variant calling tools with an array of variant filtering modules to discard unwanted

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Reading the NCBI’s GEO microarray SOFT files in R/BioConductor

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/ This page discusses how to load GEO SOFT format microarray data from the Gene Expression Omnibus database (GEO) (hosted by the NCBI) into R/BioConductor. SOFT stands for Simple Omnibus Format in Text. There are actually four[……]

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MrBayes Tree

Use clustalw to generate nexus format file #NEXUS BEGIN DATA; dimensions ntax=55 nchar=534; format missing=? symbols=”ABCDEFGHIKLMNPQRSTUVWXYZ” interleave datatype=DNA gap= -; Change to as follows: #NEXUS BEGIN DATA; dimensions ntax=55 nchar=534; format datatype=dna interleave=yes g[……]

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微生物基因组中的GC-skew(zhuantie)

如果给出两个关键词:生物信息、GC,可能很多人的第一反应是“GC含量”(GC-content)或者“CpG岛”(CpG island)吧。这两个星期开始做非编码RNA(Non-coding RNA)预测(对象是Sinorhizobium meliloti,草木樨中华根瘤菌),接触到一个以前没听说过的新的“GC理论”:GC-skew.查国内文献,几乎找不到对它的详细介绍(也没有对应的中文翻译,skew有“ 歪,偏, 斜”的意思,通过我对这个理论的理解,就把GC-skew翻译为“GC偏移”吧)。这里翻译一篇Nature上的Review,和大家分享一下。                  [……]

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Install genometools

the ‘new’ error message refers to a nonexistant Cairo library on your system, which is needed for the AnnotationSketch component of GenomeTools. If you do not need this, do a ‘make cleanup’ and recompile with the additional make option ‘cairo=no’, e.g. ‘make errorcheck=no cairo=no’. This will di[……]

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DSK: k-mer counting with very low memory usage

Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of[……]

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How to measure codon usage bias

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[……]

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