Furna: a structural database for FUnctions of RNA

0. configure binary executables

cd script
make
cd cdhit_src/
make
make install

Optionally, to show directed acylic graph for Gene Ontology terms on the website, the dot program from Graphviz can be used. If your system does not have Graphviz, you can install it to graphviz/bin/dot from source code:

wget https://gitlab.com/api/v4/projects/4207231/packages/generic/graphviz-releases/6.0.2/graphviz-6.0.2.tar.gz
tar -xvf graphviz-6.0.2.tar.gz
cd graphviz-6.0.2/
mkdir ../graphviz
./configure --prefix=`readlink -e ../graphviz`
make
make install
cd ..
rm -rf graphviz-6.0.2.tar.gz graphviz-6.0.2

1. Get cisbp-RNA download link

Go to http://cisbp-rna.ccbr.utoronto.ca/bulk.php, click "Download Entire Datasets Archive", which will open http://cisbp-rna.ccbr.utoronto.ca/bulk_archive.php. Right click on "Download" and Copy link address. Paste the url link to

my $url="http://cisbp-rna.ccbr.utoronto.ca/tmp/entiredata_2023_09_25_9:33_am.zip";

at the top of script/download_cisbp.pl.

2. Download raw data

script/download_pdb.pl
script/download_rfam.pl
script/download_rnacentral.pl
script/download_goa.pl
script/download_sifts.pl

3. Curate data

script/curate_pdb.pl
script/curate_rfam.pl
script/curate_rnacentral.pl
script/curate_goa.pl
script/combine_chain.pl

4. Download data for each rna entry

script/download_pubmed.pl
script/download_assembly.pl
script/combine_interaction.pl
script/download_ligand.pl
script/combine_protein.pl
script/download_taxon.pl
script/fasta2taxon.pl
script/plot_goa.pl
script/make_summary.pl
script/combine_dna.pl
script/curate_blastdb.pl
script/download_uniprot.pl
script/download_attract.pl