├── .gitignore ├── README.md ├── _config.yml ├── data ├── 1EHZ_junctions.png ├── 1EHZ_stem_loops.png ├── 1ehz.pdb ├── 3Q1Q.png ├── ft3100_2D_with_bracket_notation.fasta ├── ft3100_from_FANTOM3_project.fasta └── telomerases.fasta ├── fabfile.py ├── grid_tasks ├── annotate.task ├── import_3Ds.task ├── let_it_sno.task ├── napp.task └── template.task ├── logo.afdesign ├── notebooks ├── Create and manipulate alignments.ipynb ├── Create and manipulate molecules.ipynb ├── Create and manipulate secondary structures.ipynb └── Create and manipulate tertiary structures.ipynb ├── pyrna ├── .DS_Store ├── __init__.py ├── computations.py ├── db.py ├── features.py ├── glite.py ├── parsers.py ├── restclient.py ├── server.py ├── task.py ├── utils.py └── websites.py ├── scripts ├── python │ ├── embl_to_fasta.py │ ├── find_cisregulatory_motifs.py │ ├── find_gene_models.py │ ├── from_genbank_ids_2_organism_names.py │ ├── genbank_ids_2_fasta_and_gff3.py │ ├── get_accession_numbers_from_taxid.py │ ├── get_rfam_ids.py │ ├── glite.py │ ├── import_3Ds.py │ ├── pyrna_tests.py │ ├── refine_snoclusters.py │ ├── rfam3ds_2_assemble2.py │ ├── rfam_seed_to_mongodb.py │ ├── rnaml_to_ct.py │ ├── rnapedia.py │ ├── sam2mongo.py │ ├── sam2soap.py │ ├── scan_genome_for_2Ds.py │ ├── search_SL1.py │ ├── split_rfam_alignments.py │ ├── svm.py │ └── trnaScanSE.py └── shell │ ├── getCDD.sh │ ├── getRfam_data.sh │ ├── getRfam_families.sh │ ├── getRfam_genomicEntries.sh │ ├── getRfam_taxonomy.sh │ ├── get_ensembl_ncrnas.sh │ └── get_rfam_families_from_jobs_list.sh ├── server_load.png ├── servers.txt └── website ├── bower.json ├── css ├── dashboard.css └── timeline.css ├── images └── booquet_logo.png ├── js ├── d3 │ ├── LICENSE │ ├── d3.layout.min.js │ └── d3.v3.min.js └── dashboard.js └── pages ├── account.html ├── booquet.html ├── index.html ├── login.html ├── pyrna.html ├── rnapedia.html ├── server.html └── webservices.html /.gitignore: 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