ARGs-OAP: 抗性基因在线分析工具(转)

ARGs_OAP_v2.0(步骤1):https://github.com/biofuture/Ublastx_stageone
ARGs-OAP在线分析网站(步骤2): http://smile.hku.hk/SARGs

无处不在的抗性基因
图片.png

环境中抗生素抗性基因(ARGs)的来源:
随机突变或表达潜在抗性基因等方式使细菌体内基因组上存在的抗性基因原型、准抗性基因或潜在抗性基因被表达出来,从而使细菌获得的抗生素抗性。
抗生素在人和动物肠道内诱导产生耐药菌,这些编码ARGs的耐药菌经由粪便排出并进入环境中,是环境中ARGs的重要来源。
抗性基因的水平转移是抗性基因在环境中传播的的主要机制,通过将包含抗性基因的质粒、转座子、整合子作为载体,通过细菌之间细胞与细胞的接触,将抗性基因从载体细胞转移到受体细胞。

如何检测环境中抗生素抗性基因(ARGs):
  • PCR技术—定性。
  • qPCR技术—定量。
  • 宏基因组测序:以环境样品中的整个微生物群体基因组为研究对象,检测环境样本微生物中的物种组成、丰度,基因预测、基因丰度,利用数据库进行注释,得到样本中ARGs的种类和丰度与样本的相关性。
  • ARDB数据库:主要包含细菌病原菌的多种抗性基因数据,不能为环境样本宏基因组数据提供详[……]

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pronunciation

发音第一个 n 带鼻音

analysis    (noun single  )

analyses (noun)  (multiplex number of analysis)

动词

analyse  a’ n(ə)lʌɪz          发音a 不带鼻音

th 在尾巴 发 f

thanks

中间ch发k的时候要弱化发音

tmap install

 

1199 git clone https://github.com/GPZ-Bioinfo/tmap.git
1200 cd tmap
1201 ll
1202 python setup.py install
1203 ll
1204 cd ../
1205 rm -rf tmap
1206 deactivate
1207 rmvirtualenv tmap_ENV
1208 mkvirtualenv -p /usr/bin/python3.4m tmap_ENV

pip3 install pypiwin32

conda install scipy

sudo pip3 install matplotlib

 

cloud cmd install

 

 

 

Install

The installation of file manager is very simple.

  • install latest version of node.js.
  • install cloudcmd via npm with:
npm i cloudcmd -g

When in trouble use:

npm i cloudcmd -g --force

sudo vi /usr/lib/node_modules/cloudcmd/json/config.json

“dirStorage”: false,
“online”: true,
“open”: false,
“keysPanel”: true,
“port”: 8080,
“ip”: “143.89.31.17”,
“root”: “/”,
“prefix”: “”,
“progress”: true,
“contact”: true,
“confirmCopy”: true,
“confirmMove”: true,
“configDialog”: true,
“oneFilePanel”: false,
“console”: true,
“syncC[……]

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Basic Usage of tmap

import sklearn

import plotly.plotly as py
import plotly.graph_objs as go

import matplotlib.pyplot as plt
import numpy as np

from sklearn.cluster import DBSCAN
from sklearn import metrics
from sklearn.datasets.samples_generator import make_blobs
from sklearn.preprocessing import StandardScaler




###################################
# Load libraries
from sklearn import datasets
from sklearn.preprocessing import StandardScaler
from sklearn.cluster import DBSCAN
from sklearn.preprocessing import MinMaxScaler

###################################



shenzy@SZYENVS:~/[......]

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Good measure to download sequence from NCBI based on acc or gi number

cat file_with_ids.txt | while read p; do echo $p; esearch -db nucleotide -query $p | efetch -format fasta > $p.fasta; done;

 

 

cat ginumber.txt| while read p; do echo $p; efetch -db nucleotide -id $p -format gb > $p.gbk; done;

 

shenzy@SZYENVS:~/work/zhongshan/virus_database$ cat ginumber.txt| while read p; do echo $p; efetch -db nucleotide -id $p -format gb > $p.gbk; done;
AY180661
AY180662
AY180663
AY180664
AY180665
AY180666
AY180667
AY180668
AY180669
AY180670
AY180671
AY180672
AY180673
AY180674
AY180675
AY180676
AY180677

VOSEQ server start

####

[shenzy@LFE0530 VoSeq-2.1.1]$ source /usr/bin/virtualenvwrapper.sh
[shenzy@LFE0530 VoSeq-2.1.1]$ workon voseq_environment
(voseq_environment) [shenzy@LFE0530 VoSeq-2.1.1]$

python voseq/manage.py runserver –settings=voseq.settings.local 143.89.29.80:8000

 

setup environmental variables, virtual environments

Wai-Yin Kwan edited this page on Jul 5, 2015 · 12 revisions

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Sci-Hub 最新可用网址

Pubmedy:显示影响因子+引用数、Sci-hub全文下载的浏览器扩展

很多人都知道一个下载文献的好地方 Sci-Hub,但是现在 Sci-Hub 的站长 Alexandra Elbakyan 女士面临着爱思唯尔的诉讼,让其面临数百万美元的赔偿。因此现在 Sci-Hub 在某些时候可能不可用了。不过 Alexandra Elbakyan 女士并未妥协,希望大家能多支持一下这位女士(貌似只能接受比特币捐款,我也不知道怎么弄,要是paypal或者payoneer就好了)。

相信很多人都知道下面这两个网址:

Sci-Hub 官网:http://www.sci-hub.org/

Sci-Hub 替代网址:http://www.sci-hub.io/

http://sci-hub.ac/和http://sci-hub.cc/也都已经阵亡(2017月12月6日测试)

以上几个网址都挂了,现在可用的是

http://sci-hub.bz/(12月8日测试 已经不可用了)

http://sci-hub.la/

http://sci-hub.hk/

http://sci-hub.tw/

http://sci-hub.tv/

http://80.82.77.83/

http://80.82.77.84/

fasta2nexus by R script

Workspace loaded from ~/.RData]

> setwd("/home/shenzy/work/beast/51samples")
> library(seqinr)
> data=read.fasta("51strain_core_gene_alignment.aln")
> library(ape)

Attaching package: ‘ape’

The following objects are masked from ‘package:seqinr’:

    as.alignment, consensus

> write.nexus.data(data,file="51strain_core_gene_alignment.aln.nexus", format="DNA")
>

change the font size of leaf nodes when generating phylogenetic trees using Bio.Phylo.draw()

axes : matplotlib/pylab axes If a valid matplotlib.axes.Axes instance, the phylogram is plotted in that Axes. By default (None), a new figure is created.

This means that you can load your own axes with your size of choice. For example

import matplotlib
import matplotlib.pyplot as plt
from Bio import Phylo
from cStringIO import StringIO

def plot_tree(treedata, output_file):
    handle = StringIO(treedata)  # parse the newick string
    tree = Phylo.read(handle, "newick")
    matplotlib.rc('font', size=6)
    # set the size of the figure
    fig = plt.figure(figsize=(10, 20), dpi=10[......]

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