Rfam簡介
Rfam是Rfam是用來鑒定non-coding RNAs的數(shù)據(jù)庫，常用于注釋新的核酸序列或者基因組序列。Rfam：http://eddylab.org/infernal/
Rfam用戶手冊：http://eddylab.org/infernal/Userguide.pdf
1. 下載infernal軟件
# infernal-1.1.1.tar.gz 下載軟
#在你安裝軟件的文件中建立一個Rfam的文件
wget http://eddylab.org/software/infernal/infernal-1.1.1.tar.gz
tar xf infernal/infernal-1.1.1.tar.gz
cd infernal/infernal-1.1.1.tar.gz
./configure --prefix=`pwd`/../infernal_bin
#安裝步驟
make
make install
cd easel; make install
cd ../../infernal_bin/bin
ls
#在該文件夾值就可以看到已安裝的文件
export PATH=${PATH}:`pwd` #改變環(huán)境變量
2.下載數(shù)據(jù)庫
wget ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam.cm.gz
gunzip Rfam.cm.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.2/Rfam12.2.claninfo
#使用infernal中的cmpress引索Rfam.cm
../infernal_bin/bin/cmpress Rfam.cm #我的必須進(jìn)入到該文件家中進(jìn)行
#輸出文件
Working... done.
Pressed and indexed 2588 CMs and p7 HMM filters (2588 names and 2588 accessions).
Covariance models and p7 filters pressed into binary file: Rfam.cm.i1m
SSI index for binary covariance model file: Rfam.cm.i1i
Optimized p7 filter profiles (MSV part) pressed into: Rfam.cm.i1f
Optimized p7 filter profiles (remainder) pressed into: Rfam.cm.i1p
#表示完成
3. 查詢待測基因組的大小【必須】
../infernal_bin/bin/esl-seqstat ~/M.truncatula/Medtr_v4_0v1/JCVI.Medtr.v4.20130313.fasta
#輸出
Format: FASTA
Alphabet type: DNA
Number of sequences: 230
Total # residues: 532015 #該行是我們需要的數(shù)字考慮到基因組為雙鏈和下一步用到的參數(shù)的單位為Million，我們使用公式532015* 2 / 1000000計算得出結(jié)果為1.06403，作為下一步參數(shù)-Z的值.
Smallest: 202
Largest: 21302
Average length: 2313.1
運行
# Rfam12.2.claninfo 為下載的claninfo文件，需提供所在路徑
# Rfam.cm 下載的cm文件
# my-genome.fa 待查詢序列
# my-genome.cmscan 輸出結(jié)果
# my-genome.tblout 有一個輸出結(jié)果
cmscan -Z `esl-seqstat my-genome.fa | awk '{if($0~/^Total/) print int($4/2000000);}''` --cut_ga --rfam --nohmmonly --tblout my-genome.tblout --fmt 2 --clanin Rfam12.2.claninfo Rfam.cm my-genome.fa > my-genome.cmscan
#根據(jù)參考博客的博主命令如上，但是自己的運行時總是報錯，出不了結(jié)果
根據(jù)官網(wǎng)給出的使用手冊
image.png
根據(jù)使用手冊運行的
~/software/infernal_bin/bin/cmscan ~/software/Rfam/Rfam.cm ../candidate_fasta/CPC_fasta/u_cpc.fasta
#
cmscan :: search sequence(s) against a CM database
# INFERNAL 1.1.1 (July 2014)
# Copyright (C) 2014 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file: ../candidate_fasta/CPC_fasta/u_cpc.fasta
# target CM database: /root/software/Rfam/Rfam.cm
# number of worker threads: 1
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: XLOC_000318::chr1:4780155-4784203() [L=4048]
Hit scores:
rank E-value score bias modelname start end mdl trunc gc description
---- --------- ------ ----- ---------- ------ ------ --- ----- ---- -----------
------ inclusion threshold ------
(1) ? 0.14 15.6 1.0 snR73 2280 2346 + hmm - 0.30 -
(2) ? 0.17 18.2 0.2 sroH 2044 1992 - cm no 0.25 -
(3) ? 1.5 12.2 0.2 Afu_328 3042 3012 - hmm - 0.29 -
(4) ? 5.5 10.7 1.6 adapt33_1 3099 3052 - hmm - 0.23 -
(5) ? 5.8 18.7 0.0 SNORD19 3298 3375 + cm no 0.40 -
(6) ? 6.5 16.5 0.1 snoR66 2441 2506 + cm no 0.26 -
(7) ? 7.6 9.3 2.3 DLX6-AS1_2 136 241 + hmm - 0.33 -
(8) ? 9.4 23.9 0.2 KRAS_3UTR 1432 1501 + cm no 0.26 -
Hit alignments:
>> snR73
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ? 0.14 15.6 1.0 hmm 1 67 [. 2280 2346 + .. 0.66 - 0.30
::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::.::::::: CS
snR73 1 GUUUAUGAUGAuUucCacUU.aUCACGACGGUCAaCUGcGuUcuUCgAuUGUUUAuuuaaG.aACuUUG 67
GUU A GAUGAuUu a+UU +UCA C GUCAaCUG+G U+u C+ UG UUA a+G +A uUU
XLOC_000318::chr1:4780155-4784203() 2280 GUUGAGGAUGAUUUUUAUUUaUUCAUAUCUGUCAACUGUGAUUUCCU--UGAUUAAACAGGuGAGUUUA 2346
5778899******6666555499*****************9988774..55555544333323333333 PP
......................
在這步，卡住了
后續(xù)再繼續(xù)...............
[2019.8.20]
參考：本地使用Rfam
