Source 1primary paper2014Nucleic Acids Research
Toolkit/SwiftLib
SwiftLib
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
SwiftLib is a computational method for optimizing degenerate codon libraries using dynamic programming. It is designed to rapidly generate degenerate-codon-library designs and was reported to improve on an existing integer-linear programming formulation for this task.
Usefulness & Problems
Why this is useful
SwiftLib is useful for designing degenerate codon libraries and is reported to provide rapid optimization through a dynamic programming approach. The method is also freely available through a web server, which supports practical access to the design workflow.
Source:
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
Source:
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
Problem solved
SwiftLib addresses the computational problem of optimizing degenerate codon library designs. The available evidence specifically indicates that it improves on an existing integer-linear programming formulation for this design task.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
dynamic programmingTechniques
Computational DesignTarget processes
No target processes tagged yet.
Implementation Constraints
SwiftLib is available through a web server. Beyond its use of dynamic programming for degenerate codon library optimization, the supplied evidence does not specify software requirements, input parameterization, or integration with downstream library synthesis workflows.
The supplied evidence does not describe the optimization objective, benchmark scope, codon constraints, or experimental validation of resulting libraries. It also does not provide details on supported inputs, output formats, or performance across different protein engineering use cases.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
SwiftLib is freely available through a web server.
Our algorithm is freely available through our web server
SwiftLib is freely available through a web server.
Our algorithm is freely available through our web server
SwiftLib is freely available through a web server.
Our algorithm is freely available through our web server
SwiftLib is freely available through a web server.
Our algorithm is freely available through our web server
SwiftLib is freely available through a web server.
Our algorithm is freely available through our web server
SwiftLib is freely available through a web server.
Our algorithm is freely available through our web server
SwiftLib is freely available through a web server.
Our algorithm is freely available through our web server
SwiftLib improves on an existing integer-linear programming formulation for degenerate codon library design.
improving on the existing integer-linear programming formulation
SwiftLib improves on an existing integer-linear programming formulation for degenerate codon library design.
improving on the existing integer-linear programming formulation
SwiftLib improves on an existing integer-linear programming formulation for degenerate codon library design.
improving on the existing integer-linear programming formulation
SwiftLib improves on an existing integer-linear programming formulation for degenerate codon library design.
improving on the existing integer-linear programming formulation
SwiftLib improves on an existing integer-linear programming formulation for degenerate codon library design.
improving on the existing integer-linear programming formulation
SwiftLib improves on an existing integer-linear programming formulation for degenerate codon library design.
improving on the existing integer-linear programming formulation
SwiftLib improves on an existing integer-linear programming formulation for degenerate codon library design.
improving on the existing integer-linear programming formulation
SwiftLib can find near-perfect libraries in which the ratio of amino-acid sequences to nucleic-acid sequences approaches 1.
the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1
amino acid sequence to nucleic acid sequence ratio 1
SwiftLib can find near-perfect libraries in which the ratio of amino-acid sequences to nucleic-acid sequences approaches 1.
the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1
amino acid sequence to nucleic acid sequence ratio 1
SwiftLib can find near-perfect libraries in which the ratio of amino-acid sequences to nucleic-acid sequences approaches 1.
the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1
amino acid sequence to nucleic acid sequence ratio 1
SwiftLib can find near-perfect libraries in which the ratio of amino-acid sequences to nucleic-acid sequences approaches 1.
the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1
amino acid sequence to nucleic acid sequence ratio 1
SwiftLib can find near-perfect libraries in which the ratio of amino-acid sequences to nucleic-acid sequences approaches 1.
the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1
amino acid sequence to nucleic acid sequence ratio 1
SwiftLib can find near-perfect libraries in which the ratio of amino-acid sequences to nucleic-acid sequences approaches 1.
the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1
amino acid sequence to nucleic acid sequence ratio 1
SwiftLib can find near-perfect libraries in which the ratio of amino-acid sequences to nucleic-acid sequences approaches 1.
the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1
amino acid sequence to nucleic acid sequence ratio 1
In two examined library-design problems, using multiple degenerate codons produced libraries that very nearly covered the desired amino acid set while staying within experimental size limits.
In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits.
In two examined library-design problems, using multiple degenerate codons produced libraries that very nearly covered the desired amino acid set while staying within experimental size limits.
In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits.
In two examined library-design problems, using multiple degenerate codons produced libraries that very nearly covered the desired amino acid set while staying within experimental size limits.
In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits.
In two examined library-design problems, using multiple degenerate codons produced libraries that very nearly covered the desired amino acid set while staying within experimental size limits.
In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits.
In two examined library-design problems, using multiple degenerate codons produced libraries that very nearly covered the desired amino acid set while staying within experimental size limits.
In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits.
In two examined library-design problems, using multiple degenerate codons produced libraries that very nearly covered the desired amino acid set while staying within experimental size limits.
In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits.
In two examined library-design problems, using multiple degenerate codons produced libraries that very nearly covered the desired amino acid set while staying within experimental size limits.
In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits.
SwiftLib extends degenerate codon library design to consider multiple degenerate codons at each position while adhering to a constraint on the number of primers needed for library synthesis.
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
SwiftLib extends degenerate codon library design to consider multiple degenerate codons at each position while adhering to a constraint on the number of primers needed for library synthesis.
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
SwiftLib extends degenerate codon library design to consider multiple degenerate codons at each position while adhering to a constraint on the number of primers needed for library synthesis.
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
SwiftLib extends degenerate codon library design to consider multiple degenerate codons at each position while adhering to a constraint on the number of primers needed for library synthesis.
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
SwiftLib extends degenerate codon library design to consider multiple degenerate codons at each position while adhering to a constraint on the number of primers needed for library synthesis.
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
SwiftLib extends degenerate codon library design to consider multiple degenerate codons at each position while adhering to a constraint on the number of primers needed for library synthesis.
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
SwiftLib extends degenerate codon library design to consider multiple degenerate codons at each position while adhering to a constraint on the number of primers needed for library synthesis.
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
SwiftLib provides a dynamic programming solution for finding degenerate codons while keeping library size below a specified limit.
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
SwiftLib provides a dynamic programming solution for finding degenerate codons while keeping library size below a specified limit.
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
SwiftLib provides a dynamic programming solution for finding degenerate codons while keeping library size below a specified limit.
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
SwiftLib provides a dynamic programming solution for finding degenerate codons while keeping library size below a specified limit.
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
SwiftLib provides a dynamic programming solution for finding degenerate codons while keeping library size below a specified limit.
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
SwiftLib provides a dynamic programming solution for finding degenerate codons while keeping library size below a specified limit.
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
SwiftLib provides a dynamic programming solution for finding degenerate codons while keeping library size below a specified limit.
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
SwiftLib solves most design problems in about a second.
solves most design problems in about a second
runtime about a second
SwiftLib solves most design problems in about a second.
solves most design problems in about a second
runtime about a second
SwiftLib solves most design problems in about a second.
solves most design problems in about a second
runtime about a second
SwiftLib solves most design problems in about a second.
solves most design problems in about a second
runtime about a second
SwiftLib solves most design problems in about a second.
solves most design problems in about a second
runtime about a second
SwiftLib solves most design problems in about a second.
solves most design problems in about a second
runtime about a second
SwiftLib solves most design problems in about a second.
solves most design problems in about a second
runtime about a second
Approval Evidence
1 source7 linked approval claimsfirst-pass slug swiftlib
SwiftLib: rapid degenerate-codon-library optimization through dynamic programming
Source:
availabilitysupports
SwiftLib is freely available through a web server.
Our algorithm is freely available through our web server
Source:
comparative performancesupports
SwiftLib improves on an existing integer-linear programming formulation for degenerate codon library design.
improving on the existing integer-linear programming formulation
Source:
design efficiencysupports
SwiftLib can find near-perfect libraries in which the ratio of amino-acid sequences to nucleic-acid sequences approaches 1.
the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1
Source:
design outcomesupports
In two examined library-design problems, using multiple degenerate codons produced libraries that very nearly covered the desired amino acid set while staying within experimental size limits.
In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits.
Source:
method capabilitysupports
SwiftLib extends degenerate codon library design to consider multiple degenerate codons at each position while adhering to a constraint on the number of primers needed for library synthesis.
It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library.
Source:
method capabilitysupports
SwiftLib provides a dynamic programming solution for finding degenerate codons while keeping library size below a specified limit.
This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit
Source:
runtimesupports
SwiftLib solves most design problems in about a second.
solves most design problems in about a second
Source:
Comparisons
Source-backed strengths
The reported strengths are rapid degenerate-codon-library optimization and improved performance relative to an existing integer-linear programming formulation. A further practical strength is that the method is freely available through a web server.
Source:
improving on the existing integer-linear programming formulation
Ranked Citations
- 1.