Summary: Non-canonical nucleic and amino acid monomers are essential to enhance the information capacity, functional capabilities, and stability of DNA, RNA, and protein biopolymers. However, there are few tools for describing the primary structure of biopolymers that include non-canonical monomers. We developed BpForms , the first toolkit for concretely and compactly describing the primary structures of non-canonical 1-dimensional biopolymers. BpForms includes the first alphabets of non-canonical DNA, RNA, and protein monomers; a FASTA-like notation for describing biopolymers; and a website, a command line program, a REST API, and a Python package for calculating properties of biopolymers. We anticipate BpForms will be a valuable tool for communicating data about modified DNA, RNA, and proteins, as well as integrating data about epigenetic, post-transcriptional, and post-translational modification.BpForms will also be valuable for whole-cell modeling and cell engineering. Availability and implementation: BpForms is freely available open-source at URL
Although non-canonical residues, caps, crosslinks, and nicks play an important role in the function of many DNA, RNA, proteins, and complexes, we do not fully understand how networks of non-canonical macromolecules generate behavior. One barrier is our limited formats, such as IUPAC, for abstractly describing macromolecules. To overcome this barrier, we developed BpForms and BcForms, a toolkit of ontologies, grammars, and software for abstracting the primary structure of polymers and complexes as combinations of residues, caps, crosslinks, and nicks. The toolkit can help quality control, exchange, and integrate information about the primary structure of macromolecules into fine-grained global networks of intracellular biochemistry.
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Summary: Non-canonical nucleic and amino acid monomers are essential to enhance the information capacity, functional capabilities, and stability of
Although non-canonical residues, caps, crosslinks, and nicks play an important role in the function of many
R
and protein biopolymers. However, there are few tools for describing the primary structure of biopolymers that include
proteins, and complexes, we do not fully understand how networks of
R
monomers. We developed BpForms , the first toolkit for concretely and compactly describing the primary structures of non-canonical 1-dimensional biopolymers. BpForms includes the first alphabets of non-canonical DNA, RNA, and protein monomers; a FASTA-like notation for describing biopolymers; and a website, a command line program, a REST API, and a Python package for calculating properties of biopolymers. We anticipate BpForms will be a valuable tool for communicating data about modified DNA, RNA, and proteins, as well as integrating data about epigenetic, post-transcriptional, and post-translational modification.BpForms will also be valuable for whole-cell modeling and cell engineering. Availability and implementation: BpForms is freely available open-source at URL
macromolecules generate behavior. One barrier is our limited formats, such as IUPAC, for abstractly describing macromolecules. To overcome this barrier, we developed BpForms and BcForms, a toolkit of ontologies, grammars, and software for abstracting the primary structure of polymers and complexes as combinations of residues, caps, crosslinks, and nicks. The toolkit can help quality control, exchange, and integrate information about the primary structure of macromolecules into fine-grained global networks of intracellular biochemistry.