31 results about "Genomic annotation" patented technology

A computer-based genomic annotation system, including a database configured to store genomic data, non-transitory memory configured to store instructions, and at least one processor coupled with the memory, the processor configured to implement the instructions in order to implement an annotation pipeline and at least one module filtering or analysis of the genomic data.

A computer-based genomic annotation system, including a database configured to store genomic data, non-transitory memory configured to store instructions, and at least one processor coupled with the memory, the processor configured to implement the instructions in order to implement an annotation pipeline and at least one module filtering or analysis of the genomic data.

The invention discloses a method for batch inspection of plant genome LTR-retrotransposon. An LTR_STRUC program based on structural characteristics and searching from the beginning, a CROSS_MATCH program based on homology searching and a CLUSTALW comparison program based on sequence similarity are comprehensively applied in the method for the batch inspection of the plant genome LTR-retrotransposon, and Perl scripting language programming and other methods are combined. Experimental results show that the method for the batch inspection of the plant genome LTR-retrotransposon is relatively systematic, the effect for detecting the direct repeat of the inserting sites of the plant genome LTR-retrotransposon is good, speed is high, and process operation is easy to achieve. According to the method, the frequently-used software for detecting the plant genome LTR-retrotransposon and the Perl scripting language programming are combined, and certain defects of the frequently-used software are made up. The method can play an important role in genome annotation and the batch inspection of the plant genome LTR-retrotransposon.

A genome-scale metabolic network reconstruction for Clostridium acetobutylicum (ATCC 824) was created using a new semi-automated reverse engineering algorithm. This invention includes algorithms and software that can reconstruct genome-scale metabolic networks for cell-types available through the Kyoto Encyclopedia of Genes and Genomes. This method can also be used to complete partial metabolic networks and cell signaling networks where adequate starting information base is available. The software may use a semi-automated approach which uses a priori knowledge of the cell-type from the user. Upon completion, the program output is a genome-scale stoichiometric matrix capable of cell growth in silico. The invention also includes methods for developing flux constraints and reducing the number of possible solutions to an under-determined system by applying specific proton flux states and identifying numerically-determined sub-systems. Although the model-building and analysis tools described in this invention were initially applied to C. acetobutylicum, the novel algorithms and software can be applied universally.

The invention discloses a method for screening a regulation new gene participating in the biological process. A biologic informatics method is used for searching gene ontology for a tool, and the semantic relation in the specific biological process is screened out; in a genome annotation database of different species, gene set information in different species annotated to the semantic is screenedout; homology analysis is performed on the gene set information of the specific species, an orthologous gene in the species to be researched is screened out; comparison and analysis are performed on the gene and the reference gene participating in the biologic process in the species to be researched, and the regulation new gene participating in the biologic process in the specific species is screened out. On the basis that the specific biologic process has the advantage of high conservative property between different species, a method for screening the regulating new gene participating in thebiologic process is built, the supporting effect is supplied for further reconstructing a systematic gene regulation network, and the method is of a great significance in early disease diagnosis, individual treatment and medicine development.

The invention relates to the genome sequencing technology field and especially relates to a method for accurately predicting a BSA-seq candidate gene in a low-density SNP genomic region. BSA-seq has alow-density SNP region near a candidate interval. Through comparing SNPs between two parents, an SNP list is strictly filtered to find a low-density region, and then, a corresponding candidate interval when a confidence interval is 95% and a low-density candidate interval are used, and a genome annotation website is used to annotate the genes in a candidate region. A candidate region variation point function is annotated so as to obtain a gene with functional variation such as frameshift variation and the like, and the gene is determined to be a candidate gene. The method can be used to makeup for the false positive of the candidate region due to the region with a small difference in a genome, and the real candidate interval is acquired.

A computer-based genomic annotation system, including a database configured to store genomic data, non-transitory memory configured to store instructions, and at least one processor coupled with the memory, the processor configured to implement the instructions in order to implement an annotation pipeline and at least one module filtering or analysis of the genomic data.

A computer-based genomic annotation system, including a database configured to store genomic data, non-transitory memory configured to store instructions, and at least one processor coupled with the memory, the processor configured to implement the instructions in order to implement an annotation pipeline and at least one module filtering or analysis of the genomic data.

The invention relates to the technical field of genome annotation, and provides a genome annotation method using second-generation and third-generation transcriptome sequencing data. The method of the present invention includes the following steps: Step 1: align the three-generation full-length transcriptome sequencing sequence to the target genome to obtain the initial structural information of each coding gene; Step 2: align the second-generation transcriptome sequencing short sequence to the target genome Genome, extract intron splicing site information from the comparison file; step 3: combine the initial structure information of each coding gene and intron splicing site information to obtain the final structure information of each coding gene. The present invention can not only make full use of the advantage of high accuracy that the full-length transcript sequence can be obtained without splicing the third-generation transcriptome, but also fully consider the advantage that the second-generation transcriptome sequencing data can provide a large number of intron splicing site evidences , greatly improving the accuracy and efficiency of genome annotation.

The invention discloses a method for batch inspection of plant genome LTR-retrotransposon. An LTR_STRUC program based on structural characteristics and searching from the beginning, a CROSS_MATCH program based on homology searching and a CLUSTALW comparison program based on sequence similarity are comprehensively applied in the method for the batch inspection of the plant genome LTR-retrotransposon, and Perl scripting language programming and other methods are combined. Experimental results show that the method for the batch inspection of the plant genome LTR-retrotransposon is relatively systematic, the effect for detecting the direct repeat of the inserting sites of the plant genome LTR-retrotransposon is good, speed is high, and process operation is easy to achieve. According to the method, the frequently-used software for detecting the plant genome LTR-retrotransposon and the Perl scripting language programming are combined, and certain defects of the frequently-used software are made up. The method can play an important role in genome annotation and the batch inspection of the plant genome LTR-retrotransposon.

A computer-based genomic annotation system, including a database configured to store genomic data, non-transitory memory configured to store instructions, and at least one processor coupled with the memory, the processor configured to implement the instructions in order to implement an annotation pipeline and at least one module filtering or analysis of the genomic data.

The invention relates to a promoter query method, system and equipment of a species genome, the method comprises obtaining the genome file, genome annotation file and fastq file of the species; according to the genome annotation file, sorting all the genes in the genome file to obtain Species promoter files; use hisat2 or Trinity software to convert fastq files into FPKM files containing highly expressed genes; use steps S1 to S3 to obtain species promoter files and FPKM files of several species, and pass the species promoter files of several species and FPKM files to build a promoter database. The promoter query method of the genome of this species can query the promoters of the required genes in the promoter database, does not limit the query of gene promoters of any species, does not require additional auxiliary tools, and the accuracy of the promoters obtained from the query is high .