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KarrLab
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bpforms
Toolkit for concretely describing non-canonical DNA, RNA, and proteins
https://www.bpforms.org
MIT License
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Can `bpforms` visualize the svg strings from biopolymers?
#111
paulflang
closed
3 years ago
1
Residues on the protein alphabet website do not bond to left or right
#110
paulflang
closed
3 years ago
5
Recognize the equivalence of circularity and crosslinks which generate circular molecules.
#109
paulflang
opened
3 years ago
3
Error building from Dockerfile
#108
paulflang
opened
3 years ago
2
Make it easier to describe sequences
#107
jonrkarr
opened
4 years ago
0
Represent additional types of uncertainty
#106
jonrkarr
opened
4 years ago
0
Contribute PRO and MODOMICS analysis to h1 project
#105
jonrkarr
closed
4 years ago
1
Format alphabets and ontology in OBO format and submit to BioPortal
#104
jonrkarr
closed
4 years ago
1
Capture more chemical nuances of inter-residue bonds, crosslinks, and nicks
#103
jonrkarr
closed
4 years ago
1
Represent knicks
#102
jonrkarr
closed
4 years ago
1
Remove crosslinks from protein alphabet
#101
jonrkarr
closed
4 years ago
1
Enhance test coverage
#100
jonrkarr
closed
4 years ago
1
Generate CML, visualizations for PRO
#99
jonrkarr
closed
4 years ago
1
Add method that returns difference between two polymers
#98
jonrkarr
closed
4 years ago
1
Add method to generate sequence visualizations
#97
jonrkarr
closed
4 years ago
1
Add comments to crosslinks
#96
jonrkarr
closed
4 years ago
1
Add BcForms to docs
#95
jonrkarr
closed
5 years ago
1
Merge PDB CCD DNA and RNA residues in alphabets
#94
jonrkarr
closed
4 years ago
2
Use ontology to abstract away atomic details of crosslinks
#93
jonrkarr
closed
4 years ago
1
Move limits on size to REST module
#92
jonrkarr
closed
5 years ago
1
Allow white space at end of notation
#91
jonrkarr
closed
5 years ago
1
Make standard EBNF version of grammar
#90
jonrkarr
closed
5 years ago
1
Return coordinate information with Bpform.get_structure
#89
jonrkarr
closed
5 years ago
1
Fix opacity of displaced atoms
#88
jonrkarr
closed
5 years ago
1
Throw error for describing crosslink multiple times
#87
jonrkarr
closed
5 years ago
1
Allow line breaks in syntax
#86
jonrkarr
closed
5 years ago
1
Simplify alphabets by eliminating backbones
#85
jonrkarr
closed
5 years ago
1
Merge REPAIRtoire with DNA alphabet
#84
jonrkarr
closed
5 years ago
1
Speed up loading BpForms
#83
jonrkarr
closed
5 years ago
2
Add utility method for reading from FASTA file
#82
jonrkarr
closed
5 years ago
1
Rename `get_fasta` to `get_canonical_seq`
#81
jonrkarr
closed
5 years ago
1
Propose SEP for integration with SBOL
#80
jonrkarr
closed
5 years ago
1
Link to grammar from website
#79
jonrkarr
closed
5 years ago
1
Clarify notation on website
#78
jonrkarr
closed
5 years ago
1
Cache JSON for HTML pages
#76
jonrkarr
closed
5 years ago
1
Generate images of structures with monomer, backbone, bond coloring
#75
jonrkarr
closed
5 years ago
1
Move image generation from REST to install script on website
#74
jonrkarr
closed
5 years ago
1
Fix identification of protein N and C termini
#73
jonrkarr
closed
5 years ago
1
Add documentation to website
#72
jonrkarr
closed
5 years ago
1
Add examples to website
#71
jonrkarr
closed
5 years ago
1
Speed up alphabet HTML pages with PNG images
#70
jonrkarr
closed
5 years ago
1
Case studies
#69
jonrkarr
closed
5 years ago
1
Add comparison to other resources to docs
#68
jonrkarr
closed
5 years ago
1
Rename "monomer" --> "monomeric form" in documentation to enhance clarity
#67
jonrkarr
closed
5 years ago
1
Support inter-monomer bonds (e.g. disulfide bonds)
#66
jonrkarr
closed
5 years ago
2
Add more info to alphabet HTML pages
#65
jonrkarr
closed
5 years ago
2
Build consensus alphabets
#64
jonrkarr
closed
5 years ago
2
Support left/right only bonding
#63
jonrkarr
closed
5 years ago
1
Explore integration with BioPAX
#62
jonrkarr
closed
5 years ago
1
Allow left/right only bonding
#61
jonrkarr
closed
5 years ago
1
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