工商网站查询企业信息查询官网,wordpress4.8版权修改,免费网站推广2023,大连旅游网站建设大概多钱KEGG数据库#xff0c;即京都基因和基因组百科全书(Kyoto Encyclopedia of Genes and Genomes)#xff0c;是系统分析基因功能、基因组信息的数据库。KofamKOALA是一个方便的KEGG功能注释工具#xff0c;由创建KEGG的京都大学化研所生物信息中心学者在2019年11月发表于Bioin…KEGG数据库即京都基因和基因组百科全书(Kyoto Encyclopedia of Genes and Genomes)是系统分析基因功能、基因组信息的数据库。KofamKOALA是一个方便的KEGG功能注释工具由创建KEGG的京都大学化研所生物信息中心学者在2019年11月发表于Bioinformatics。以隐马尔科夫模型(HMM)创建的KOfam来进行蛋白序列同源搜索其准确性可与性能最佳的工具相媲美 有网页和Linux两个版本本文重点介绍Linux版的安装与使用。网页版网址 https://www.genome.jp/tools/kofamkoala/avatar网页填入蛋白序列信息设值E值和留下邮箱点击Compute只需要等待邮箱回复Linux版Linux版本的KofamKOALA 需要下载 KOfam(数据库)和 KofamScan(软件)软件依赖RubyHMMER和GNU Parallel(事先没有安装可以看以下教程)安装我们以kofamscan安装在主目录$HOME(或者叫~)下为例介绍step1下载和解压 KOfam 和 KofamScanmkdir -p ~/kofamscan/dbcd ~/kofamscan/dbwget ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz gunzip ko_list.gz tar xvzf profiles.tar.gz mkdir -p ~/kofamscan/bincd ~/kofamscan/binwget ftp://ftp.genome.jp/pub/tools/kofamscan/kofamscan-1.2.0.tar.gz # 注意kofamscan版本tar xvzf kofamscan-1.2.0.tar.gzstep2下载 Ruby HMMER GNU Parallelcd ~/kofamscan mkdir ruby hmmer parallel src cd src# Ruby版本应不小于2.4,这里演示的是2.7版;HMMER应大于3.1这里是3.3;Parallel为最新版wget https://cache.ruby-lang.org/pub/ruby/2.7/ruby-2.7.0.tar.gzwget http://eddylab.org/software/hmmer/hmmer-3.3.tar.gzwget ftp://ftp.gnu.org/gnu/parallel/parallel-latest.tar.bz2安装 Rubycd ~/kofamscan/src tar xvzf ruby-2.7.0.tar.gz cd ruby-2.7.0./configure --prefix$HOME/kofamscan/ruby make make install安装 HMMERcd ~/kofamscan/src tar xvzf hmmer-3.3.tar.gz cd hmmer-3.3./configure --prefix$HOME/kofamscan/hmmer make make install安装 GNU Parallelcd ~/kofamscan/src tar xvjf parallel-latest.tar.bz2 cd parallel-20190322 # 这里根据版本而定./configure --prefix$HOME/kofamscan/parallel make make install将Ruby路径加入环境变量(之后执行如果报错可能是ruby的问题推荐ruby按照本文方法安装)export PATH$HOME/kofamscan/ruby/bin:$PATHstep3复制config-template.yml文件并重命名为config.ymlcd ~/kofamscan/bin/ cp config-template.yml config.ymlcat config.yml文件,内容如下:我们需要在config.yml添加键值以便ruby识别读取.可以vim编辑加入以下内容到config.yml注意绝对路径.profile: /path/to/home/kofamscan/db/profiles ko_list: /path/to/home/kofamscan/db/ko_list hmmsearch: /path/to/home/kofamscan/hmmer/bin/hmmsearch parallel: /path/to/home/kofamscan/parallel/bin/parallel如若hummsearch和parallel可安装在其他地方改为相关路径使用现在可以使用了我们准备蛋白序列fasta文件(注意必须是蛋白序列不支持核酸序列)./exec_annotation -o result.txt query.fasta如我在~/kofamscan/test/文件夹下有samples.fasta文件定义输出文件为res.txtcd ~/kofamscan/bin/kofamscan-1.2.0 # 路径中有exec_annotation文件./exec_annotation -o ~/kofamscan/test/res.txt~/kofamscan/test/samples.fasta运行完毕后的输出文件若报错可能是ruby的路径不在首选环境变量可执行export PATH$HOME/kofamscan/ruby/bin:$PATH./exec_annotation -h查看全部参数## Options- -o FILE - The result are output to FILE. It defaults to stdout.- -p, --profilePROFILE - Use PROFILE as a profile database. See [Profiles](#profiles)- -k, --ko-listFILE - Use FILE as a KO list.- --cpuN - Set the number of hmmsearch processes started simultaneously to N. It defaults to 1 unless it is set in config.yml.- -c FILE - Use FILE as a config file instead of config.yml in the same directory as exec_annotation.- --tmp-dirDIR - Use DIR as a temporary directory where hmmsearch results are. It will be created if not exist. It defaults to ./tmp.- -E, --e-valueVALUE - Require E-value to be smaller than or equal to VALUE. If not, an asterisk will not be added in detail format or the hit will not be reported in other formats.- -T, --threshold-scaleVALUE - The score thresholds are multiplied by VALUE. For example, with -T2 option, the thresholds become twice as strict.- -f, --formatFORMAT - Set the format of the output to FORMAT. Three formats below are available. - detail - Default format. Gene name, assigned K number, threshold of the KO, hmmsearch score and E-value, and the definition of KO are shown. In addition, an asterisk * is added to the head of the line if the score is higher than the threshold. - mapper - Format which can be used for [KEGG Mapper](https://www.genome.jp/kegg/mapper.html) input. It includes a gene name and an assigned K number separated by a tab. Here, an assigned K number represents a hit with score above the predefined threshold. Note that for some KOs, predefined score thresholds are not available when they are represented by a very few number of sequences in KEGG GENES. - mapper-oneline - Similar to mapper, but when more than one KO are assigned to a gene, all assigned KO are shown in one line separated by tabs.- --[no-]report-unannotated - With --report-unannotated option, gene names are shown even when no KO is assigned (default when --formatmapper(-oneline)). With --no-report-unannotated such genes are not shown at all (default when --formatdetail).- --create-alignment - hmmsearchs normal outputs per profile are stored in the temporary directory. In addition, domain information and alignments in the outputs will be rearranged per query. - Not compatible with --reannotation- -r, --reannotation - Skip hmmsearch and assume that hmmsearch outputs are already in the temporary directory. This will help you to make an output in a different format or redo annotation changing thresholds. - Not compatible with --create-alignment- -h, --help - Show brief help message.参考 https://www.genome.jp/tools/kofamkoala/https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz859/5631907猜你喜欢10000菌群分析宝宝与猫狗梅毒狂想曲 提DNA发NatureCell专刊肠道指挥大脑系列教程微生物组入门 Biostar 微生物组 宏基因组专业技能学术图表高分文章生信宝典 不可或缺的人一文读懂宏基因组 寄生虫益处 进化树必备技能提问 搜索 Endnote文献阅读 热心肠 SemanticScholar Geenmedical扩增子分析图表解读 分析流程 统计绘图16S功能预测 PICRUSt FAPROTAX Bugbase Tax4Fun在线工具16S预测培养基 生信绘图科研经验云笔记 云协作 公众号编程模板:Shell R Perl生物科普:肠道细菌人体上的生命生命大跃进 细胞暗战 人体奥秘写在后面为鼓励读者交流、快速解决科研困难我们建立了“宏基因组”专业讨论群目前己有国内外5000 一线科研人员加入。参与讨论获得专业解答欢迎分享此文至朋友圈并扫码加主编好友带你入群务必备注“姓名-单位-研究方向-职称/年级”。PI请明示身份另有海内外微生物相关PI群供大佬合作交流。技术问题寻求帮助首先阅读《如何优雅的提问》学习解决问题思路仍未解决群内讨论问题不私聊帮助同行。学习16S扩增子、宏基因组科研思路和分析实战关注“宏基因组”点击阅读原文
