93 results about "Genome wide analysis" patented technology

The present invention provides the use of transposases and transposon ends to generate extensive fragmentation and 5′-tagging of double-stranded target DNA in vitro, followed by the use of DNA polymerases to generate 5′- and 3′-tagged single DNA without PCR amplification reactions. Methods, compositions and kits for stranded DNA fragments, wherein the first label on the 5' end shows the sequence of the transferred transposon end and optionally an additional arbitrary sequence, and the second label on the 3' end shows the same The first tab shows a sequence different from the sequence. The method can be used to generate 5' and 3' tagged DNA fragments for use in a variety of processes including metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and including massively parallel DNA sequencing (so-called "next generation sequencing") involves the process of comparative genome sequencing (CGS).

The method for genome analysis translates the clinical findings in the patient into a comprehensive test order for genes that can be causative of the patient's illness, delimits analysis of variants identified in the patient's genome to those that are “on target” for the patient's illness, and provides clinical annotation of the likely causative variants for inclusion in a variant warehouse that is updated as a result of each sample that is analyzed and that, in turn, provides a source of additional annotation for variants. The method uses a genome sequence having the steps of entering at least one clinical feature of a patient by an end-user, assigning a weighted value to the term based on the probability of the presence of the term, mapping the term to at least one disease by accessing a knowledge base containing a plurality of data sets, wherein the data sets are made up of associations between (i) clinical features and diseases, (ii) diseases and genes, (iii) genes and genetic variants, and (iv) diseases and gene variants, assigning a truth value to each of the mapped terms based on the associated data sets and the weighted value, to provide a list of results of possible diagnoses prioritized based on the truth values, with continuous adjustment of the weightings of associations in the knowledge base based on updating of each discovered diagnosis and attendant clinical features, genes and gene variants. This method can be performed in fifty hours or twenty-four hours or less.

The present invention provides parallel methods for determining nucleotide sequences of polynucleotides associated with sample tags. Applications of sequence information acquired by these methods are also provided.

The invention discloses a method for preparing a salvia miltiorrhiza EST-SSR molecular mark. The method mainly comprises the following steps of obtaining and pre-processing a salvia miltiorrhiza EST sequence, screening a SSR locus in the salvia miltiorrhiza EST sequence, designing and synthesizing the salvia miltiorrhiza EST-SSR primer, screening the salvia miltiorrhiza EST-SSR primer and the like. The method excavates the SSR locus aiming at the salvia miltiorrhiza EST and designs the PCR primer according to the flanking sequence of the SSR locus, and on the basis of this, the salvia specificEST-SSR mark system is established; and the method lays a solid foundation for genetic diversity evaluation, genetic relationship or idioplasmatic identification, genetic linkage description, molecular mark auxiliary selection, gene mapping cloning, functional genome analysis, related researches and the like of related species of the salvia miltiorrhiza and the salvia. The invention also discloses the EST-SSR locus specific primer obtained by the method for preparing the salvia miltiorrhiza EST-SSR molecular mark and the application thereof.

The invention discloses an optimized method for analyzing microbial communities through metagenome binning. The method comprises the following steps of: filtering sequencing data to obtain high-quality sequencing data, selecting different assembly strategies to obtain contigs according to the source of a sample and the sequencing data volume, and analyzing gene data. Compared with the prior art, the method disclosed by the invention is used for simultaneously carrying out biological information analysis on the whole community and single-bacterium genome analysis independent of isolated cultureaiming at the microbial community. According to the invention, on the metagenome level, an efficient high-quality assembly algorithm which is more suitable for sample characteristics and sequencing data volume is provided, rich and comprehensive information analysis content is contained, and individuality and novelty are visualized; and the method realizes metagenome analysis qualitative change from communities to single bacteria, and the scheme comprises data correction capable of improving accuracy and comprehensive and perfect bin information summarization, is beneficial to screening valuable target bins more conveniently and efficiently, and further comprises systematically perfect mining ideas of subsequent analysis of the target bins.

A method is provided for producing motif-specific, context-independent antibodies that recognize a plurality of peptides or proteins within a genome that contain the same post-translationally modified motif. The method includes the step of immunizing a host with a degenerate peptide library antigen featuring (i) a fixed target motif containing one or more invariant amino acids including at least one modified amino acid, and (ii) a plurality of degenerate amino acids flanking the motif. Motif-specific, context-independent antibodies produced by the disclosed method are also provided. The method encompasses motifs consisting of a single modified amino acid, as well as short motifs comprising multiple invariant amino acids including one or more modified amino acids, such as all or part of kinase consensus substrate motifs, protein-protein binding motifs, or other cell signaling motifs. Methods of using the antibodies, e.g. for genome-wide profiling, are also provided.

Techniques for storing omics data that indicates long sequences of elements associated with a particular biological molecule include receiving digital omics data comprising over two kilobytes. The digital omics data is split into multiple partitions. The maximum partition size is much less than then a number of elements in a typical instance of the particular biological molecule. Each partition is encrypted. Each encrypted partition is inserted into a corresponding data packet that includes an owner field that uniquely indicates an owner of the omics data. Each data packet is uploaded into a non-centralized, peer-to-peer distributed storage network. Thus, genome data is encrypted and stored in a distributed, scalable, fully decentralized, fast, and highly secure network. The network further provides for decentralized computing, trustless validation of the genomes by way of oracles and trustless genome analysis by third party providers through smart contracts.

The present disclosure provides methods of characterizing one or more microorganisms and kits for characterizing at least one microorganism. Exemplary methods include preparing an amplicon library, sequencing a characteristic gene sequence to obtain a gene sequence, and characterizing the one or more microorganisms based on the gene sequence using a computer-based genomic analysis of the gene sequence. Exemplary kits include at least one forward primer including an adapter sequence and a priming sequence, for a target sequence, and at least one reverse primer.

The invention discloses a method for detecting microorganisms in a sample, which belongs to the technical field of metagenome analysis and comprises the following steps: S1, acquiring metagenome sequencing data of the sample; and S2, performing species analysis on the metagenome sequencing data. The method further comprises a step of carrying out drug resistance gene analysis on the metagene sequencing data of the sample. The invention also discloses a system for detecting microorganisms and drug-resistant genes in a sample. On the basis of a comprehensive and accurate database and an intelligent analysis and screening algorithm, pathogenic microorganisms and drug-resistant genes are effectively identified by utilizing a metagenome sequencing method, false positive is effectively reduced,bacteria suspected to correspond to the detected drug-resistant genes can be prompted, and better technical support is provided for accurate diagnosis and treatment of infection; in addition, according to the method and the system, potential new pathogenic microorganisms can be accurately analyzed, and technical support is provided for early warning of new infectious diseases.

Genome-wide analysis of copy number changes in breast and colorectal tumors used approaches that can reliably detect homozygous deletions and amplifications. The number of genes altered by major copy number changes—deletion of all copies or amplification of at least twelve copies per cell—averaged thirteen per tumor. These data were integrated with previous mutation analyses of the Reference Sequence genes in these same tumor types to identify genes and cellular pathways affected by both copy number changes and point alterations. Pathways enriched for genetic alterations include those controlling cell adhesion, intracellular signaling, DNA topological change, and cell cycle control. These analyses provide an integrated view of copy number and sequencing alterations on a genome-wide scale and identify genes and pathways that are useful for cancer diagnosis and therapy.

Systems and methods for metagenomic analysis are provided. A method of metagenome sequence analysis of two or more samples can include (i) counting the abundance of each k-mer deconstructed from sequencing reads of nucleic acids in each sample, and (ii) using a vector space model to compute the genetic distance between each of the two or more samples according to the abundance of the k-mers. In some embodiments, counting includes (a) constructing a k-mer histogram containing the distribution of k-mers for each sample, and (b) dividing k-mers into partitions having approximately an equal number of k-mers based on the histogram, preparing an inverted index of the k-mers in each partition, and assigning a weight to each k-mer according to its abundance. Method of developing diagnostic and prognostic information using the methods of sequence analysis are also provided.

The invention discloses a rapid annotation method and device for a bacterial DNA sequence. The method comprises the following steps: respectively constructing a ResDB database, an ISDB database, an IntegronDB database and a TranssposonDB database; obtaining a bacteria DNA sequence to be analyzed; comparing the bacteria DNA sequence to be analyzed with one or more of a ResDB database, an ISDB database, an IntegronDB database and a TranssposonDB database by using a BLASTN program; and according to the coverage rate and consistency of comparison, obtaining comparison fragment sequence informationof the optimal matching gene and the query gene corresponding to the optimal matching gene, and outputting an annotation result. The method is helpful for simplifying and optimizing the current genome analysis process and accelerating the subsequent genome analysis.

The present invention provides a method for rapidly detecting the genome-wide presence of palindrome formation. The method has demonstrated that somatic palindromes occur frequently and are widespread in human cancers. Individual tumor types have a characteristic non-random distribution of palindromes in their genome and a small subset of the palindromic loci are associate with gene amplification. The disclosed method can be used to define the plurality of genomic DNA palindromes associated with various tumor types and can provide methods for the classification of tumors, and the diagnosis, early detection of cancer as well as the monitoring of disease recurrence and assessment of residual disease.

The invention discloses a method for detecting a macro virus group in a sample, and belongs to the technical field of metagenome analys.The method comprises the steps that second-generation sequencing data and third-generation sequencing data of a to-be-detected sample are mutually corrected and mixed and assembled to obtain mixed and assembled contigs, and the third-generation sequencing data are independently assembled to obtain Nanopore contigs; further, the mixed assembly contigs and the Nano-virus contigs are respectively subjected to comparison and annotation, so that candidate virus contigs, non-virus contigs and Nano-virus contigs are obtained, and the candidate virus contigs, the non-virus contigs and the Nano-virus contigs are subjected to comparison and annotation; and finally, carrying out clustering analysis on the three data sets, carrying out further comprehensive analysis according to a clustering result, supplementing missing virus sequences, and correcting a species annotation result to obtain a more sensitive, accurate and comprehensive virus identification result.

A novel transcriptome analyzing method and to provide a gene found by this method and a protein encoded by the gene. A method for determining whether or not a continued arbitrary DNA sequence existing in the genome of an arbitrary biological species, in which the nucleotide sequence is already known but its possibility of being a gene expression region is unclear (specific region), is the specific region, which comprises detecting whether or not a nucleotide sequence that corresponds to the nucleotide sequence of the region is present in the RNA of the biological species, and a method for determining the gene expression region in an arbitrary region on a genome or the entire genome, which comprises repeatedly carrying out the above method.

The invention provides an efficient sugarcane or sugarcane related species stem tip chromosome flaking method, and belongs to the technical field of cell biology. The invention provides an efficient sugarcane stem tip chromosome flaking method aiming at solving the problems that sugarcane chromosomes are large in number and small in form and ideal division phase metaphase cells are difficult to obtain through root tip flaking. Chromosome flaking is carried out by utilizing stem tip meristematic region tissues of sugarcane and sugarcane related species in a vigorous growth period, the method has the advantages of convenient material taking, large meristematic area tissue sample size, vigorous division, many metaphase cells and clear and dispersed chromosome structure, and the technical keypoints of material selection, pretreatment, fixation, dissociation dyeing, flaking and chromosome morphology microscopic observation are disclosed. The method is simple and convenient, accurate and reliable in result, good in repeatability, easy to operate and short in experiment period and improves the sugarcane chromosome genome analysis efficiency. Technical support is provided for sugarcane chromosome karyotype research, germplasm resource classification identification and protection utilization.

The present disclosure relates to methods for constructing polynucleotide libraries and/or polynucleotide sequencing. Related kits and devices are also disclosed. The present disclosure also relates to compositions, kits, devices, and methods for conducting genetic and genomic analysis, for example, by polynucleotide sequencing. In particular aspects, provided herein are compositions, kits, and methods for constructing libraries with improved ligation efficiency and conversion rate during sequencing. In certain embodiments, the compositions, kits, and methods herein are useful for analyzing polynucleotide fragments, such as circulating polynucleotide fragments in the body of a subject, Including circulating tumor DNA

The invention relates to the field of biological information, and discloses a metagenome sequencing data automatic analysis method, which comprises the steps of original offline data filtering and quality control, host genome comparison, intestinal flora species annotation and comparison, intestinal flora metabolic potential analysis, result statistics and output and the like. Python script connection is used in all the steps to achieve automatic analysis, tedious manual operation is reduced, and various errors caused by manual operation are reduced. The analysis content of the automatic analysis method covers most of metagenome analysis content, the analysis requirements of researchers can be met, intermediate results generated in all steps can be output during operation of the process, corresponding data can be subjected to statistical analysis and arrangement, a corresponding chart can be output, browsing of a user is facilitated, and meanwhile, the process operation log records allprocess related information, so that screening can be conveniently carried out when process operation errors occur.