Methods, systems, and devices are contemplated for assembling a genome from duplicate segments of the genome. Sequences with a first level of common neighboring base pairs are identified and organized into first level groups. Groups are then identified from the first level groups that have a second level of common neighboring base pairs and organized into a number of second level groups. A third level of groups can further be organized in some embodiments. Typically the second level groups are assembled into spans having contiguous base pair sequences, which are then assembled into the broader genome sequence. The inventive subject matter is preferably used for whole genome sequencing.

Methods, systems, and devices are contemplated for assembling a genome from duplicate segments of the genome. Sequences with a first level of common neighboring base pairs are identified and organized into first level groups. Groups are then identified from the first level groups that have a second level of common neighboring base pairs and organized into a number of second level groups. A third level of groups can further be organized in some embodiments. Typically the second level groups are assembled into spans having contiguous base pair sequences, which are then assembled into the broader genome sequence. The inventive subject matter is preferably used for whole genome sequencing.

Synthetic auxotrophs with one or more ligand-dependent essential gene functions and methods of production that can be used for biosafety. The ligand-dependent function of an essential gene product can be produced by a series of mutations in the ORF of an essential gene; N, C, or insertional fusions of ligand-binding domains with essential genes or an engineered ligand-dependent intein splicing to alter essential gene function. A positive and/or negative selection can be used to identify auxotrophs from created mutant libraries. The positive selection is performed by growing a mutant library in conditions where growth or viability depends on the function of mutagenized essential genes. The negative selection eliminates constitutively growing cells that do not require a ligand for growth by growing the library in the absence of complementing ligand and in conditions where growing cells are eliminated. Desirable phenotypes are collected after the selections.

A binding agent to a target molecule, or method or kit where the binding agent is selected from a library where each variant has a circular permutation of the FHA domain where the rearrange does not substantially disrupt the FHA domain's beta-sheet scaffold or increase the stability of the beta-sheet scaffold. The randomized regions of the FHA domain include the endogenous binding interface the FHA domain, the region opposite of the endogenous binding interface, and the circular permutation region.

This disclosure provides, among other things, a composition comprising: comprising a fusion protein comprising: (a) a DNA polymerase; and (b) a heterologous sequence-specific DNA binding domain. A method for copying a DNA template, as well as a kit for performing the same, are also described.

Provided herein are compositions, devices, systems and methods for the generation and use of biomolecule-based information for storage. Additionally, devices described herein for de novo synthesis of nucleic acids encoding information related to the original source information may be rigid or flexible material. Further described herein are highly efficient methods for long term data storage with 100% accuracy in the retention of information. Also provided herein are methods and systems for efficient transfer of preselected polynucleotides from a storage structure for reading stored information.

The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.

The invention provides methods for generating pools of variants of DNA templates, and methods of using pools of variants to identify sequences involved in conferring sensitivity or resistance to environmental factors.

Methods and compositions are provided for assembly of large nucleic acids where the assembled large nucleic acids lack internal sequence modifications made during the assembly process.

In certain embodiments, this disclosure relates to conjugates comprising GM-CSF and IL-4 and uses related thereto, e.g., enhancing the immune system. Typically, the GM-CSF and IL-4 are connected by a linker. In certain embodiments, the disclosure relates to isolated nucleic acids encoding these polypeptide conjugates, vectors comprising nucleic acid encoding polypeptide conjugates, and protein expression systems comprising these vectors such as infectious viral particles and host cells comprising such a nucleic acid.