The present invention discloses a sequencing library comprising a nucleotide sequence. The sequence comprises a linker sequence and two target sequences. Two ends of the linker sequence are respectively linked to the target sequences and the two target sequences are direct repeat sequences. The present invention further discloses preparation and use of the sequencing library. The present invention overcomes the high error rate problem of current DNA sequencing technologies, especially in a way of very low coverage bias, and can be used to detect low frequency mutations in different kinds of samples.

The invention relates to control compositions for sequencing and for chemical analyses, such as analytical chemistry analyses. More particularly, the invention relates to control compositions for sequencing and for chemical analyses having at least one barcode sequence fragment and at least one universal sequence fragment, and to methods of their use.

Systems, methods, and apparatuses for generating and using machine learning models using genetic data. A set of input features for training the machine learning model can be identified and used to train the model based on training samples, e.g., for which one or more labels are known. As examples, the input features can include aligned variables (e.g., derived from sequences aligned to a population level or individual references) and/or non-aligned variables (e.g., sequence content). The features can be classified into different groups based on the underlying genetic data or intermediate values resulting from a processing of the underlying genetic data. Features can be selected from a feature space for creating a feature vector for training a model. The selection and creation of feature vectors can be performed iteratively to train many models as part of a search for optimal features and an optimal model.

Methods for identifying biosynthetic gene clusters that include genes for producing compounds that interact with specific target proteins are disclosed. Some methods relate to bioinformatics methods for identifying and/or prioritizing biosynthetic gene clusters. Related systems, components, and tools for the identification and expression of such gene clusters are also disclosed.

The present disclosure provides chimeric primers suitable for use in the amplification of a nucleic acid sequence. In some aspects, these chimeric primers reduce the formation of primer dimers and/or off-target amplification products, compared to amplification reactions carried out using unmodified primers.

In accordance with some embodiments, systems, methods, and media for determining relative quality of oligonucleotide preparations. In some embodiments, a system comprises a processor programmed to: (a) receive genetic sequencing results for multiple libraries with target concentrations of oligonucleotides; (b) calculate at least one prediction band; (c) repeat (a) and (b) for multiple preparations; (d) determine boundaries for a final prediction band based on the prediction bands calculated at (b) for each of the preparations; and (e) present a report indicative of quality of the libraries, including metrics indicative of the final prediction band.

Molecular beacons and developmental methods related thereto. Methods include obtaining a nucleotide sequence for an aptamer that binds to a target analyte. The aptamer comprises a binding domain nucleotide sequence, a first domain nucleotide sequence, and a displacement domain nucleotide sequence complementary to the first domain nucleotide sequence. A molecular beacon is developed based on the nucleotide sequence of the aptamer by preserving the binding domain nucleotide sequence and truncating or extending one or both of the first domain nucleotide sequence or the displacement domain nucleotide sequence. The resultant molecular beacon is developed such that the molecular beacon comprises a Gibbs free energy value that is greater than the Gibbs free energy value of the aptamer.

Disclosed are methods for identifying bio-molecules with desired properties (or which are most suitable for a round of directed evolution) from complex bio-molecule libraries or sets of such libraries. Some embodiments of the present disclosure provide methods for virtually screening proteins for beneficial properties. Some embodiments of the present disclosure provide methods for virtually screening enzymes for desired activity and/or selectivity for catalytic reactions involving particular substrates. Some embodiments combine screening and directed evolution to design and develop proteins and enzymes having desired properties. Systems and computer program products implementing the methods are also provided.

A system for producing a therapeutic oligomer includes a computing device configured to design a proposed therapeutic oligomer sequence, wherein designing further comprises generating a genomic library for an organism from a gene target, initiating a sequence identification function, identifying a genomic locus that the proposed therapeutic oligomer sequence is predicted to bond to as a function of an off-target sequence function, selecting the proposed therapeutic oligomer sequence as a function of the sequence identification function, the genomic locus, and a criterion element, and synthesize a therapeutic oligomer as a function of the proposed therapeutic oligomer sequence.

A system for producing a therapeutic oligomer includes a computing device configured to design a proposed therapeutic oligomer sequence, wherein designing further comprises generating a genomic library for an organism from a gene target, initiating a sequence identification function, identifying a genomic locus that the proposed therapeutic oligomer sequence is predicted to bond to as a function of an off-target sequence function, selecting the proposed therapeutic oligomer sequence as a function of the sequence identification function, the genomic locus, and a criterion element, and synthesize a therapeutic oligomer as a function of the proposed therapeutic oligomer sequence.