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Amber generate file of inpcrd problem

source leaprc.ff10 loadamberparams frcmod.ionsjc_tip3p set default PBradii mbondi2 1vom = loadpdb 1vom-clean.pdb addions 1vom Na+ saveamberparm 1vom prmtop inpcrd

########### resolve a problem

export AMBERHOME=`pwd` root@shenzy-pc:/home/shenzy/lib/amber14# ./update_amber –apply leap.patch export AMBERHOME=`pwd` ./update_amber –apply http://ambermd.org/bugfixes/AmberTools/13.0/cygwin_fix

root@shenzy-pc:/home/shenzy/lib/amber14# cat leap.patch *******>leap.patch

Author: Jason Swails

Date: 30 April, 2014

Programs: tleap, xleap

Description: Solves potential inpcrd file truncation […]

gff3 to gft method

The easiest way is to use the gffread program that comes with the Cufflinks software suite (Tuxedo)

gffread my.gff3 -T -o my.gtf

See gffread -h for more information

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Toward more realistic drug–target interaction predictions

Toward more realistic drug–target interaction predictions.

STAMP (Statistical Analysis of Metagenomic Profiles)

STAMP

Using STAMP to identify SEED subsystems which are differentially abundant between CandidatusAccumulibacter phosphatis sequences obtained from a pair of enhanced biological phosphorus removal (EBPR) sludge metagenomes(data originally described in Parks and Beiko, 2010).

STAMP (Statistical Analysis of Metagenomic Profiles) is a software package for analyzing metagenomic profiles (e.g., a taxonomic profile indicating the […]

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA […]

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 the integrated network by entering keywords and BEReX returns a sub-network matching the keywords. […]

Mothur 命令手册-Mothur命令中文解释

Mothur命令中文解释——Mothur中文简易教程 Mothur命令教程从这个页面http://www.mothur.org/wiki/Category:Commands 上查阅的所有命令，根据个人理解翻译了一下。个人能力有限，会有不当之处。

A-G (查看时请用Ctrl+F快捷键)

Align.check 这个命令使你计算16S rRNA基因序列中潜在的错配碱基对数目。如果你对ARB(http://www.arb-home.de/)的编辑窗口熟悉的话，这与计算~，#，-和=这些符号的数目相同。用greengenes的二级结构图谱和esophagus dataset运行这个命令。要运行这个命令，你必须提供FASTA格式的序列文件。 Align.seqs 这个命令把用户提供的FASTA格式的候选序列文件对齐到用户提供的同样格式的模板序列。通用的方法是： 1.采用kmer searching（http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page），blastn或suffix tree searching找到每个候选序列的最接近模板 2.在候选序列文件和空位模板序列之间进行碱基配对，采用Needleman-Wunsch，Gotoh，或者blastn算法规则。 3.重新在候选和模板序列对之间插入间隔（空位），采用NAST算法，这样候选序列就能与原始模板序列兼容。我们提供了一些16S和18S基因序列的数据库，这些是与greengenes和SILVA队列兼容的。然而，自定义的任何DNA序列的排列都可以用作模板，所以鼓励用户分享他们的排列供其他人使用。普遍来说，进行排列是很快的-我们能在3小时内将超过186000个的全长序列排序到SILVA排列中，而且质量像SINA aligner做的一样好。另外，这个速率可以由多个处理器加倍。 Amova 分子方差分析（Analysis of molecular variance）是一种传统方差分析的非参数模拟。这种方法被广泛应用在种群遗传学以检测关于两个种群的遗传多样性不是显著不同于由这两个种群的共同联合导致的多样性这样一个假设。 Anosim 参考文献：Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143. 群落结构变化的非参数多元分析《澳大利亚生态学报》 Bin.seqs 这个命令输出一个fasta格式的文件，其中序列根据它们所属的OTU进行排序。这样的输出也许对一个OTU生成特异性引物有帮助，用来对序列进行分类。 Catchall 这个命令使mothur与Linda Woodard，Sean Connolly和John Bunge开发的catchall程序连接。获取更多信息，请参看http://www.northeastern.edu/catchall/index.html。catchall的可执行程序必须与你的mothur在同一个文件夹里。如果你是一个Mac或Linux用户，你必须也安装了mono，在catchall的网页中有一个关于mono的链接。 Chimera.bellerophon 采用Bellerophon方法生成一个挑选的优先嵌合序列的得分列表。 Chimera.ccode […]

PyroHMMvar: a sensitive and accurate method to call short INDELs and SNPs for Ion Torrent and 454 data

Motivation: The identification of short indels and SNPs from Ion Torrent and 454 reads is a challenging problem, essentially because these techniques are prone to sequence erroneously at homopolymers and can, therefore, raise indels in reads. Most of the existing mapping programs do not model homopolymer errors when aligning reads against the reference. The […]

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 similar/noisy NGS reads or sequences inference of ancestral sequences

PAGAN documentation is available at the […]

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

http://sourceforge.net/projects/cakesomatic/

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