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
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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
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). 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 […]
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 […] 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! ############################################## 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: […] 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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