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 the integrated network by entering keywords and BEReX returns a sub-network matching the keywords. […]
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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 similar/noisy NGS reads or sequences inference of ancestral sequences
PAGAN documentation is available at the […] # 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}’
# 打印文件的最后一行 （模拟 “tail -1″） awk ‘END{print}’ […]
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
http://sourceforge.net/projects/cakesomatic/ 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 types of GEO SOFT file available: GEO Platform (GPL) These files describe a particular type of microarray. They […] 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 gap=- missing=?; then type mb -i *.nex MrBayes > lset nst=6 rates=invgamma Setting Nst to 6 Setting Rates to Invgamma Successfully […] 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 disable support for AnnotationSketch and remove the cairo […] 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 distinct k-mers to count. We present a […] 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 associated to it. shenzy@shenzy-ubuntu:~/Downloads/CondonW/codonW$ codonw input.dat -all_indices […] |
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