Rfam 数据库是一个 RNA 家族的集合，每个家族都由多个序列比对、一致二级结构和协方差模型表示。

https://rfam.org/

http://eddylab.org/infernal/

  1. conda install -c bioconda infernal

https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/

  1. # Rfam.cm
  3. wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.clanin
  4. wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz
  6. gunzip Rfam.cm.gz
  7. cmpress Rfam.cm
  8. ## Working...    done.
  9. ## Pressed and indexed 4178 CMs and p7 HMM filters (4178 names and 4178 accessions).
  10. ## Covariance models and p7 filters pressed into binary file:  Rfam.cm.i1m
  11. ## SSI index for binary covariance model file:                 Rfam.cm.i1i
  12. ## Optimized p7 filter profiles (MSV part)  pressed into:      Rfam.cm.i1f
  13. ## Optimized p7 filter profiles (remainder) pressed into:      Rfam.cm.i1p
  1. mkdir infernal
  2. cd infernal
  4. genome=../../genome.renamed.fa
  6. cmscan \
  7.   --cut_ga \
  8.   --rfam \
  9.   --nohmmonly \
  10.   --fmt 2 \
  11.   --tblout genome.tblout \
  12.   --clanin ../Rfam.clanin \
  13.   ../Rfam.cm \
  14.   ${genome}

https://github.com/nawrockie/jiffy-infernal-hmmer-scripts/blob/master/infernal-tblout2gff.pl

参考

Rfam 地址：https://rfam.xfam.org/

Rfam 介绍：https://docs.rfam.org/en/latest/about-rfam.html

使用Rfam数据库注释基因组中的非编码RNA（ncRNA）

ncRNA注释