Rfam数据库使用介绍
Genome annotation Non-coding RNA analysis using the Rfam database - PMC ncbi.nlm.nih.gov/pmc/ar Userguide.pdf eddylab.org/infernal/Us 发布于 2024-08-02 11:43・IP 属地北京 生信 RNA 生信分析 赞同1添加评论 分享喜欢收藏申请转载 ...
数据库介绍1.1数据库介绍1.1.1 什么是数据库? 简单的说,数据库(因为Database)就是一个存放数据的仓库,这个仓库是按照一定的数据结构(数据结构是指数据的组织形式或数据之间的联系)来组织、存储的,我们可以通过数据库提供的多种方式来管理数据库里的数据。 更简单形象的理解,数据库和我们 ... ...
The database can also be downloaded in flatfile form and searched locally using the INFERNAL package (http://infernal.wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide data...
The non-coding RNA famiiles database. Rfam has 17 repositories available. Follow their code on GitHub.
34 Step 3(VIII) Search Rfam Database 34.1 Overview If the query RNA is part of a family of structured RNAs, valuable information such as structure alignments, consensus secondary structures, and covariance models can be found on the Rfam database. The query sequence is scanned versus the Rfam...
cd infernal-1.1.4/ ./configure --prefix=/opt/biosoft/infernal-1.1.4/ make -j 4 make install cd .. && rm -rf infernal-1.1.4/ echo 'PATH=$PATH:/opt/biosoft/infernal-1.1.4/bin' >> ~/.bashrc source ~/.bashrc # Installing Rfam Database (http://rfam.xfam.org/) ...
在这个过程中还要计算CM database中的模型的数量 在Rfam14.4中使用: less Rfam.cm | grep 'NAME'|sort|wc -l 我得到的结果是7874 在这一步我的是单链的,所以我没有乘2; 在这个过程中,会出现一个问题就是你使用esl-seqstat命令的时候会出现如下情况: ...
Rfamis a database and collection of differentRNAfamilies, which are divided in three groups: non-codingRNA genes, structuredcis-regulatory elements and self-splicing RNAs. Each of them is represented bymultiple sequence alignments, consensussecondary structuresand covariance models (simultaneouslyRNA seque...
We have successfully tested MARNA on several datasets taken from the Rfam database.doi:10.1093/bioinformatics/bti550Sven Siebert S Siebert,R Backofen - 《Bioinformatics》 被引量: 395发表: 2005年 RNIE: Genome-wide prediction of bacterial intrinsic terminators RNIE: genome-wide prediction of bacteria...