Abstract: The invention provides methods and compositions relating to cells having altered functions, and the nucleic acids that impart those functions. Altered cellular function arises from in vivo directed recombination of genetic elements to yield a recombined nucleic acid. These methods and compositions may utilize altered host cells having altered recombination enzyme profiles and/or altered recombination sites. The invention involves in some aspects methods for assembling nucleic acid molecules, such as genomic DNA. Aspects of the invention also provide kits, compositions, devices, and systems for generating novel recombined nucleic acids and cells having altered cell function.

Abstract: A system and method for aiding in the design of molecular constructs is provided. A feature set associated with a molecular building block in a construct may be determined, wherein the feature set may comprise data indicative of third party rights that restrict use of the molecular segment or the lack of such rights. The method may include steps of defining a molecular structure for use in the construct; searching a database including a plurality of molecular structures and a plurality of rights, each right of the plurality of rights associated with each of the plurality of molecular structures; and displaying rights associated with the defined molecular structures in response to the search of said database.

Abstract: Certain aspects of the present invention provide methods for assembling nucleic acid molecules. Some embodiments involve analyzing nucleic acid sequences and determining appropriate assembly strategies based on the presence or absence of sequence features that are known or predicted to interfere with extension-based and/or ligation-based assembly techniques. Aspects of the invention also provide kits, compositions, devices, and systems for assembling synthetic nucleic acids using polymerase-based techniques, ligase-based techniques, or combinations thereof.

Abstract: Aspects of the invention provide compositions and methods for displaying engineered polypeptides on a cell surface. According to aspects of the invention, immobilized polypeptides can be screened to identify one or more variants having one or more functional or structural properties of interest. Aspects of the invention provide composition and methods for producing engineered protein or protein variants having a functional or a structural property of interest.

Abstract: Aspects of the invention relate to the design and synthesis of nucleic acid libraries containing non-random mutations or variants. Aspects of the invention provide methods for assembling libraries containing high densities of predetermined variant sequences. Certain embodiments relate to the design and synthesis of nucleic acid libraries that express a predetermined polypeptide from a library of nucleic acids having silent sequence variants. Certain embodiments relate to the design and synthesis of nucleic acid libraries that express predetermined RNA variants that encode the same polypeptide sequence.

Abstract: Aspects of the invention relate to the design and synthesis of nucleic acid libraries. Certain embodiments relate to the design and synthesis of nucleic acid libraries that express polypeptides. In some embodiments, the invention provides methods for analyzing polypeptide sequences and identifying those that may confer undesirable properties in vivo (e.g., poor solubility, high immunogenicity, low stability, etc.). In some embodiments, the invention provides methods for synthesizing a library of nucleic acids having predetermined sequences (e.g., a library of nucleic acids that encode polypeptides having related sequences with predetermined sequence variations).

Abstract: The present invention provides recombination based methods for assembling nucleic acids. In certain aspects the present invention provides hierarchical assembly methods for producing genome sized polynucleotide constructs. The methods may be used for assembling large polynucleotide constructs, for synthesizing synthetic genomes, or for introducing a plurality of nucleotide changes throughout the genome of an organism. In another aspect, the invention provides cells having increased genomic stability. For example, cells comprising alterations in at least a substantial portion of the transposons in the genome are provided.