安装软件

# 安装Rfam数据库比对软件Infernal/INFErence of RNa ALignments (http://eddylab.org/infernal/)
#wget http://eddylab.org/infernal/infernal-1.1.4.tar.gz -P ~/software/
tar zxf ~/software/infernal-1.1.4.tar.gz
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/)
# Rfam 14.1 (January 2019, 3016 families)
# Rfam 14.9 (November 2022, 4108 families)
#wget ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz -P ~/software/
mkdir -p /opt/biosoft/bioinfomatics_databases/Rfam
gzip -dc ~/software/Rfam.cm.gz > /opt/biosoft/bioinfomatics_databases/Rfam/Rfam.cm
cmpress /opt/biosoft/bioinfomatics_databases/Rfam/Rfam.cm

运行

mkdir -p /home/train/05.genome_feature_analysis/Rfam
cd /home/train/05.genome_feature_analysis/Rfam

cmsearch --cut_ga --nohmmonly --rfam --noali --cpu 8 --tblout rfam_out.tab /opt/biosoft/bioinfomatics_databases/Rfam/Rfam.cm ~/00.incipient_data/data_for_genome_assembling/assemblies_of_Malassezia_sympodialis/Malassezia_sympodialis.genome_V01.fasta  > rfam_out.txt
# real  7m8.997s
# user  42m29.662s
# sys   0m13.048s

Rfam_rRNA_stats.pl rfam_out.tab
Rfam_miRNA_stats.pl rfam_out.tab /opt/biosoft/bioinfomatics_databases/Rfam/Rfam.cm
Rfam_snRNA_stats.pl rfam_out.tab ~/software/snoRNA_type.txt

tRNA预测

软件安装

# 安装 tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/)
#wget http://trna.ucsc.edu/software/trnascan-se-2.0.12.tar.gz -P ~/software
tar zxf ~/software/trnascan-se-2.0.12.tar.gz
cd tRNAscan-SE-2.0/
./configure --prefix=/opt/biosoft/tRNAscan-SE-2.0 && make -j 4 && make install
ln -s /opt/biosoft/infernal-1.1.4/bin/* /opt/biosoft/tRNAscan-SE-2.0/bin
cd .. && rm -rf tRNAscan-SE-2.0
echo 'PATH=$PATH:/opt/biosoft/tRNAscan-SE-2.0/bin/' >> ~/.bashrc
source ~/.bashrc

tar zxf ~/software/tRNAscan-SE-1.3.1.tar.gz
cd tRNAscan-SE-1.3.1
perl -p -i -e 's#\$\(HOME\)#/opt/biosoft/tRNAscan-SE-1.3.1#' Makefile
make && make install
echo 'PATH=$PATH:/opt/biosoft/tRNAscan-SE-1.3.1/bin/' >> ~/.bashrc
echo 'export PERL5LIB=$PERL5LIB:/opt/biosoft/tRNAscan-SE-1.3.1/bin/' >> ~/.bashrc
source ~/.bashrc
make testrun
cd ..
rm tRNAscan-SE-1.3.1/ -rf

mkdir -p /home/train/05.genome_feature_analysis/tRNAscan-SE
cd /home/train/05.genome_feature_analysis/tRNAscan-SE

tRNAscan-SE -o tRNA.out -f tRNA.ss -m tRNA.stats ~/00.incipient_data/data_for_genome_assembling/assemblies_of_Malassezia_sympodialis/Malassezia_sympodialis.genome_V01.fasta
# real  0m2.087s
# user  0m2.034s
# sys   0m0.041s

tRNAscanSE2GFF3.pl tRNA.out tRNA.ss > tRNA.gff3