40 results about "Genomic databases" patented technology

The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).

The invention relates to a pathogenic microorganism genome database and an establishment method thereof, and belongs to the technical field of meta-genomes. The method comprises the following steps ofdata acquisition, wherein pathogenic microorganism genome data is obtained; strain genome screening, wherein species strain genomes are selected according to a predetermined screening rule; plasmid sequence removal, wherein plasmid sequences existing in the strain genomes obtained in the last step are removed; filtration, wherein according to a predetermined filtering rule, strains with incorrectlabeling information, incomplete chromosome assembly and incorrect classification are removed to obtain a reference strain genome of the species; fusion genome construction, wherein the reference strain genome is interrupted, redundancy is removed, reassembly is performed, and the sequences are reassembled to obtain a fusion genome of the species; database assembly, wherein the above steps are repeated to obtain the fusion genome of the predetermined species, summary is performed, and the pathogenic microorganism genome database is obtained. The genome database has the advantages of not onlyhaving a high precision rate, but also having short analysis time and reducing the cost.

A system for annotating genomic variant files includes an application server, an annotation database, a genomic database, and an annotation processing computer system. The genomic database may be graph-oriented. The annotation processing computer system processes can process variant files in batch modes and includes annotation modules designed to improve the speed of the annotation process. The batch modes may include batch transmission, and/or batch annotation.

A system for annotating genomic variant files includes an application server, an annotation database, a genomic database, and an annotation processing computer system. The genomic database may be graph-oriented. The annotation processing computer system processes can process variant files in batch modes and includes annotation modules designed to improve the speed of the annotation process. The batch modes may include batch transmission, and/or batch annotation.

The present invention relates to systems and methods for the characterization of biological material within a sample or isolate. The characterization may utilize probabilistic methods that compare sequencing information from fragment reads to sequencing information of reference genomic databases and/or trait-specific database catalogs. The characterization may be of the identities and/or relative concentrations or abundance of one or more organisms contained in the sample or isolate. The identification of the organisms may be to the species and/or sub-species and/or strain level with their relative concentrations or abundance. The characterization may additionally or alternatively be of one or more traits (i.e., characteristics) of the biological material contained in the sample or isolate. The characterization of the one or more traits may be with the relative abundance of the traits.

The present disclosure provides methods and systems for identifying variants of a given target protein or target gene that perform the same function and/or improve the phenotypic performance of a host cell transformed with such a variant. To enhance the diversity of identified candidate sequences, the methods may implement the use of a metagenomic database and/or machine learning methods. The methods and systems may be implemented in optimizing a biosynthetic pathway, e.g., to improve the production of a target molecule of interest.

The invention relates to an epinephelus coioides interferon IFNgamma1 gene, a protein coded by the gene and an application of the protein in preparing a novel immunopotentiator. According to the invention, an opened reading frame of the IFNgamma1 gene is cloned from head-kidney RNAs (Ribonucleic Acid) of epinephelus coioides through a method of screening a genome database and designing specific primer amplification. The nucleotide sequence of the gene is shown as SEQIDNO:2. The amino acid sequence of the protein coded is shown as SEQIDNO:1. Through initial verification, the epinephelus coioides interferon IFNgamma1 protein can induce associated expression of immunogenes and can be developed to natural immunopotentiators or immunologic adjuvants for fishes.

The invention relates to a multi-omics data analysis system and a data conversion method thereof. The analysis system comprises an interaction module, a processing module and a plurality of omics databases, the interaction module is used for providing an interactive form for a user so as to collect data analysis demand information of the user on one or more omics databases; the processing module is used for extracting or converting associated data matched with the analysis demand information from one or more omics databases according to the data analysis demand information and returning the associated data to the interaction module; and the plurality of omics databases includes a genomics database, a transcriptomics database, an epimics database, and a proteomics database. Different data analysis requirements of the user for one or more omics are collected in a mode of interacting with the user, and different analysis and mining of multiple omics data are realized by utilizing a mutual mapping relation of different omics data.

The invention provides a nasopharyngeal carcinoma database which comprises a clinical large database and a genomics database. The clinical large database records first data formed by clinical alphanumeric information and second data extracted and recognized according to clinical image information. The first data, the second data and/or genomics data in the nasopharyngeal carcinoma database are accompanied by the time attributes thereof. The data in the nasopharyngeal carcinoma database are used to support a diagnosis and treatment decision server to carry out diagnosis and treatment decision based on a first model, a second model, a third model, a fourth model and/or a fifth model. Multi-omics data are input into the fourth model and the fifth model. Single-omics data are input into the first model, the second model and the third model. The nasopharyngeal carcinoma database provided by the invention provides a user with accurate intelligent diagnosis decision services based on artificial intelligence, and has a broad application prospect.

Systems, methods, and computer program products are described that process inquiries or orders regarding purchase of biological devices, substances, or related reagents. In some implementations, a user selects probe-set identifiers that identify microarray probe sets capable of enabling detection of biological molecules. Corresponding genes or EST's are identified and are correlated with related product data, which is provided to the user. Further, the user may select products for purchase based on the product data. If so, the user's account may be adjusted based on the purchase order. In the same or other implementations, a local genomic database is periodically updated. In response to a user selection of probe-set identifiers, data related to corresponding genes or EST's is provided to the user from the local genomic database.

The invention discloses a sorghum 14-3-3 protein GF14a gene with a nucleotide sequence shown in SEQ ID NO.1. The invention also discloses a protein encoded by the sorghum 14-3-3 protein GF14a gene, with an amino acid sequence shown in SEQ ID NO.2. The present invention also discloses a recombinant vector comprising the above sorghum 14-3-3 protein GF14a gene and expression method of the above sorghum 14-3-3 protein GF14a gene. By the protein sequence of the corn GF14a gene, the homologous gene GF14a of sorghum is obtained from a sorghum genomic database, the gene is 780 bp in length, a prokaryotic expression vector is constructed according to the gene and is purified by a protein purification system, and the result thereof lays the foundation for further research on the crystal structure and biological characteristics of the protein, to further provide a basis for improving the stress resistance of sorghum by genetic editing methods.

The invention provides a method for compiling a genomic database for a complex disease, such as Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), and a method for using the database for identifying genetic patterns that can potentially categorize, diagnose, and/or predict therapeutics for the complex disease.

Embodiments of the invention provide a query method and system for a species genomics database. The method comprises the steps of acquiring a query instruction input by a user; performing visual operation on species underlying data in the species genomics database based on the query instruction to generate a visual operation instruction; adopting a preset analysis tool to analyze and calculate thevisual operation instruction to obtain a data analysis result; performing permission auditing on the data analysis result based on a species data auditing mechanism, and feeding back a login auditingresult to the user; and based on the login auditing result, extracting a visual return result from the species genomics database for operation management by the user. According to the embodiments ofthe invention, the method capable of realizing efficient data analysis, safe data auditing and verification and standard data management is provided for the establishment of a species genome library by adopting a method of standardizing management and analysis of data via a plurality of subsystems.

The present invention relates to use of novel bioinformatics approach for predicting and identifying Scaffold/Matrix attachment regions (S/MARs) from different genomic database.