database « 小生这厢有礼了(BioFaceBook Personal Blog)

Batch download protein sequences from CMR (comprehensive microbial resource)

NCBI 有时批量下载的protein sequence会有不一致时，可以从以下资源数据库下载（eg, eth195) http://cmr.jcvi.org/cgi-bin/CMR/shared/MakeFrontPages.cgi?page=batchdownload […]

Batch download sequences from uniprot based on protein names

Ok, I’ll do mine in English:

go to UniProt.org.
click tab “retrieve”
Paste list into text box. Click Retrieve button.
On results page, click FASTA download [ Download (30 KB*) | Open ] (Or you could click open just to have a look).

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Workflows:

Processing 16S rRNA data using a unsupervised method Processing 16S rRNA data using a supervised method Processing functional gene data using a supervised method

Individual tools:

Using the Pipeline Initial Process Align 16S rRNA sequences using Infernal Alig[……]

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Bioinformatics for personal genome interpretation

http://bib.oxfordjournals.org/content/13/4/495.full

Key Points

Vast amounts of variation data from genome sequencing studies need to be analyzed to understand its association with various phenotypes.
Well-curated databases, reliable tools for gene prioritization and accurate methods for[……]

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Databases and resources for personal genome interpretation

Database

URL

Description

Short variations—SNVs, short indels

1000 Genomes

http://www.1000genomes.org

Human short variants and inferred genotypes

dbSNP

http://www.ncbi.nlm.nih.gov/projects/SNP

Short[……]

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最近需要对预测到的基因进行个注释工作，着手进行blast2go的工作：最简单方式:运用官网的免费在线调用数据库方式，（需要安装好JAVA Java Runtime Environment (JRE) from http://www.java.com/download）步骤如下：（1）进入官网http://www.blast2go.com/b2glaunch/start-blast2go 选择相应大小的内存，点击here，如未能直接在线运行，则会让你保存并下载blast2go.jnlp 文件。（2）然后直接在命令行运行 javaws blast2g[……]

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INSTALL MicrobeDB

shenzy@shenzy-ubuntu:/usr/local/lib/perl/5.10.1/MicrobeDB/scripts$ load_genome.pl -d /home/shenzy/Downloads/unpublished_genomes/Pseudomonas_aeruginosa_LESB58/

2012/05/15 16:01:48> Working on /home/shenzy/Downloads/unpublished_genomes/Pseudomonas_aeruginosa_LESB58/

2012/05/15[……]

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小生这厢有礼了(BioFaceBook Personal Blog)

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Batch download protein sequences from CMR (comprehensive microbial resource)

Batch download sequences from uniprot based on protein names

RDP Tutorials (16s Analysis)

Contents

Workflows:

Individual tools:

Bioinformatics for personal genome interpretation

Key Points

Databases and resources for personal genome interpretation

blast2go 本地化数据库安装运行以及简单在线调用

INSTALL MicrobeDB

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Individual tools:

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