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).

RDP Tutorials (16s Analysis)

Contents

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 Aligner

Using the RDP Classifier

Using the RDP MultiClassifier

Performing Complete Linkage Clustering

–Using the […]

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 predicting the impact of variants will be essential for the interpretation of personal genomes.

Standard and unified protocols […]

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 variants from all species

HapMap

http://www.hapmap.org

Human short variants […]

blast2go 本地化数据库安装运行以及简单在线调用

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 blast2go.jnlp 回车即可出现界面，剩下的就是简单点击界面和运行了！

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本地化数据库命令行运行方式：

B2G4PIPE – Blast2GO without graphical interface

1.从http://www.blast2go.com/b2glaunch/resources

下载相应资源

http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip

http://www.blast2go.com/data/blast2go/local_b2g_db_tutorial_0809.zip

下载b2g database所需文件:

http://archive.geneontology.org/latest-full/go-assocdb-data.gz

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz

ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz

(可选,依据mysql版本)

替换b2g_db.sql 里的TYPE=MyISAM 为 ENGINE=MyISAM

同上替换go_201110-assocdb-data里:

sed -i ‘s/TYPE=MyISAM/ENGINE=MyISAM, DEFAULT CHARACTER SET latin1/’ go_201110-assocdb-data

2. 编辑后运行tutorial 里download_and_install.sh 或像下面这样手工运行:

3. 编辑并运行b2g_db.sql:

[…]

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 16:01:48> Parsing file: /home/shenzy/Downloads/unpublished_genomes/Pseudomonas_aeruginosa_LESB58/Pseudomonas_aeruginoas_LESB58.gbk 2012/05/15 16:01:48> Can’t find file:/home/shenzy/Downloads/unpublished_genomes/NCBI_completegenomes.txt . GenomeProject table will not contain much organism information. 2012/05/15 16:01:48> Can’t find file:/home/shenzy/Downloads/unpublished_genomes/NCBI_completegenomes.txt . GenomeProject table will be missing a few fields of information. DBD::mysql::st execute failed: Unknown column ‘distance_calculated’ in ‘field list’ at […]

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