Способ обработки геномной последовательности путем выравнивания длины сидов (seed).

Provided are systems and methods for processing a genome sequence by adjusting seed length. Exemplary systems for processing a genome sequence may include a seed extractor configured to extract a seed from a target sequence; and an index generator configured to index the seed extracted from the seed extractor. In some embodiments, the length of the seed extracted is adjusted based on the number of seeds extracted from the target sequence that have the same nucleotide sequence.

Метод и состав для определения количества индивидуальных полинуклеотидных молекул в одинаковом регионе генома в одном образце. Присоединение DBR (дегенерированная область основания) прикрепляется к стартовым полинуклеотидным молекулам, которые затем секвенируются, например после этого происходит амплификация или обогащение. Несколько DBR последовательностей могут использоваться для определения последовательности полинуклеотидов. Применяется для анализа, приложений, повышает точность приложений для генотипирования.

Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.

Нанотопографическая платформа обратного захвата для доставки нуклеиновых кислот. Используется для внутриклеточной доставки нуклеиновых кислот в клетки млекопитающих, в том числе в стволовые клетки. Как пример, система может быть использована для доставки коротких рибонуклеиновых кислот (siRNA) в нервные клетки и повысить нейрональную дифференцировку стволовых клеток.

This application discloses a nanotopography-mediated reverse uptake (NanoRU) platform useful for intracellular delivery of nucleic acids into mammalian cells, in particular stem cells, as well as methods of preparation and applications thereof. In particular, this system can be used to deliver small interfering ribonucleic acids (siRNAs) into neural stem cells and enhance neuronal differentiation of the stem cells.

Метод и способ для таргетного обогащения последовательности нуклеиновых кислот в образце аминокислот и создания библиотек для NGS next generation sequencing. Особенно для продукции и захвата готовых к амплификации, таргет-специфичных интересующих участков известной нити ДНК (кодирующей, некодирующей).

The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA.

Методы для обработки референсной последовательности. Алгоритм, позволяющий вставить рид в референсную последовательность при нехватке одного или нескольких нуклеотидов или при наличии неизвестных нуклеотидов.

Provided are systems and methods for processing a reference sequence. Exemplary systems for processing a reference sequence may include a seed extractor configured to extract a seed from a reference sequence; a determiner configured to determine whether an unidentified base is present or absent in a seed extracted by the seed extractor; and an index generator configured to add a seed to an index when unidentified bases are absent from an extracted seed.

Electronic sequencing A method for sequencing nucleic acid molecules a) amplifies nucleic acid molecules and b) sequences the amplified nucleic acid molecules. Steps (a) and (b) are carried out on an array of field effect transistor (FET) sensor elements, comprising an array of nanowires. Within the array, each FET may include at least one nanowire, or one each FETs can lie between two nanowires, or one nanowire of a nanowire pair is a nanowire FET, with nucleic acids bound to a nanowire surface. A chip includes one or more arrays of field effect transistor sensor elements. A kit for sequencing nucleic acid molecules, may include one or more amplifying reagents or sequencing reagents.

Systems and methods for data analysis are provided. In one embodiment, a method for analysis is provided, including electronically receiving sequence data; electronically receiving one or more reference data sequences related to at least an expression vector; associating the sequence data with at least one of the reference data sequences to identify a transgene flanking sequence; searching a genome for one or more insertion sites of the transgene flanking sequence; and annotating the genome and the one or more insertion sites within the genome when one or more insertion sites are found in said searching step.

A computer-implemented method for annotation of a biological sequence, comprising: applying a classifier to determine a label for the first segment of a first biological sequence of a first species based on an estimated relationship between second segments in a training set and known labels of the second segments in the training set. The classifier is trained using the training set to estimate the relationship, and the second segments are of a second biological sequence of a second species that is different to, or a variant of, the first species. This disclosure also concerns a computer program and a computer system for annotation of a biological sequence.