5.2.Structure Motif

1) workflow

2) running steps

(1) get interested sequences and background sequences

文件和软件获取方式

(2) BEAM

http://beam.uniroma2.it/home

docker exec -it -u root motif bash
# 在这个路径下已经准备了练习文件
cd /home/test/motif/structure_motif/BEAM

(2.1) use RNAfold to get dot-bracket

Compute the best (MFE) structure for this sequence (primary sequence with dot-bracket)

RNAfold <test.fa >dot.fa
less dot.fa
# 查看生成的序列及点括号文件dot.fa

(2.2) get file with BEAR notation ---> fastB (fastBEAR).

awk '/^>/ {print; getline; print; getline; print $1}' dot.fa >dot_to_encode.fa
java -jar /home/test/software/BEAM/beam-2.0/BearEncoder.new.jar dot_to_encode.fa BEAMready.fa

(2.3) get structure motifs

java -jar /home/test/software/beam-2.0/BEAM_release_1.5.1.jar -f BEAMready.fa -w 10 -W 40 -M 3
cd /home/test/motif/structure_motif/BEAM/risultati/BEAMready/webLogoOut/motifs
weblogo -a 'ZAQXSWCDEVFRBGTNHY' -f BEAMready_m1_run1_wl.fa -D fasta \
-o out.jpeg -F jpeg --composition="none" \
-C red ZAQ 'Stem' -C blue XSW 'Loop' -C forestgreen CDE 'InternalLoop' \
-C orange VFR 'StemBranch' -C DarkOrange B 'Bulge' \
-C lime G 'BulgeBranch' -C purple T 'Branching' \
-C limegreen NHY 'InternalLoopBranch'
cp out.jpeg /data
# 进入share文件夹查看输出结果

example output

3) other tools

  • RNApromo

https://genie.weizmann.ac.il/pubs/rnamotifs08/64bit_exe_rnamotifs08_motif_finder.tar.gz

  • GraphProt

modelling binding preferences of RNA-binding proteins: https://github.com/dmaticzka/GraphProt

  • RNAcontext

A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins: http://www.cs.toronto.edu/~hilal/rnacontext/

4) Homework

  • 解释可视化的structure motif中不同字符的含义。可参考相应的文献或是网站。