16 results about "Representative sequences" patented technology

The invention provides a heuristic biological sequence clustering method based on semi-global comparison. The method comprises the following steps: firstly, reading all biological sequences, removing repetitive sequences, and carrying out descending sorting on the biological sequences according to sequence lengths; a first sequence is used as a representative sequence of a first category, then a next sequence is read, the similarity between the current sequence and the representative sequence is calculated by adopting a semi-global sequence comparison algorithm, each sequence can be compared to the most similar area in the representative sequence through semi-global sequence comparison, the similarity between the sequences is found to the maximum extent, and the similarity between the sequences and the representative sequence is calculated. Obtaining a relatively high comparison similarity value between the sequences; if the similarity meets a clustering threshold value, adding the similarity into a category with the same representative sequence, otherwise, taking the similarity as a new representative sequence, and generating a new category; repeating the steps until all the sequences are processed; the number of the final representative sequences is the number of clustering categories, and the categories which are the same as the representative sequences are member sequences of each category.

The embodiment of the invention provides a female vaginal flora structure typing method, device and equipment based on a consensus matrix and a storage medium, and relates to the technical field of biological detection.The method comprises the steps that based on extracted DNA of a plurality of female vaginal secretion swabs, PCR amplification is conducted through a 16s rRNA primer, sequencing and clustering are conducted on each amplified DNA, and the DNA of the female vaginal secretion swabs is obtained; the method comprises the following steps: generating ASV representative sequences, classifying and annotating the generated ASV representative sequences to obtain relative abundance matrix data of female vaginal flora, repeatedly sampling samples and strains of the relative abundance matrix data according to a set proportion, and clustering a plurality of generated subsets by adopting a plurality of clustering methods to obtain a plurality of clustering results; adopting a consensus matrix method to obtain a co-occurrence rate of any two samples in the relative abundance matrix data in a plurality of clustering results; all the obtained co-occurrence rates are clustered, and a flora CST typing result is obtained, so that the robustness and accuracy of female vagina flora structure typing are improved.

A method of the present invention includes: performing clustering on a sample sequence, the clustering including the following: grouping base sequences having 100% similarity with each other, for the sample sequences thereby to generate a primary OTU (Operational Taxonomic Unit); and further performing the clustering on the sample sequences thereby to generate a secondary OTU composed of a sequence of a predetermined centroid, and sample sequences that have a similarity larger than or equal to a predetermined threshold value with the sequence of the centroid. Here, the predetermined threshold value is less than 100%. The method further includes: setting a sequence of a primary OTU having the largest number of sequences among the primary OTUs included in each secondary OTU, as a representative sequence of the secondary OUT; collating the representative sequence with a database; and thereby estimating a lineage of the secondary OTU.

This application relates to the field of microbial detection technology, specifically to a method for detecting and analyzing the drug resistance of Mycobacterium tuberculosis based on edge computing. The method includes: classifying sequencing data of biological samples based on a metagenomic reference database to obtain a matching dataset aligned to Mycobacterium tuberculosis; extracting representative sequences of each amplified fragment from multiple amplified fragments in the first region based on the matching dataset; and performing a first alignment of the representative sequences of each amplified fragment with a mycobacterium reference database to identify Mycobacterium tuberculosis complexes based on sequence similarity. This method is suitable for operation on edge devices. The method proposed in this application, through process optimization, enables accurate, efficient, and low-cost detection of mycobacteria even with limited computing resources, thereby helping to prevent and control the spread of tuberculosis.

This application discloses a primer design method, system, and computer storage medium based on nucleic acid consistency. The method includes: obtaining a target nucleic acid sequence; classifying the target nucleic acid sequence to obtain multiple taxonomic units; using at least one target nucleic acid sequence from each taxonomic unit as a representative sequence; designing candidate primers for the representative sequence; sequentially selecting at most one pair of candidate primers from each taxonomic unit to establish a candidate primer pool; and excluding candidate primers in the candidate primer pool that exhibit non-specific amplification to obtain the final primer pool. This application is simple to operate and can handle large nucleic acid libraries, making it particularly suitable for universal primer design for pathogen libraries. Compared to similar software, the method in this application is more systematic and comprehensive, resulting in a primer pool with high coverage and low host contamination rate.

The invention discloses a feature importance comprehensive screening method, system and equipment, and belongs to the technical field of feature screening. Comprising the following steps: calculating feature importance by using various different methods to obtain various different feature sequences; through four methods of counting, Spearman, Kendall and cosine similarity, the similarity between each pair of feature sequences is calculated, and four groups of similarity matrixes are formed; performing weighted summation on the four groups of similarity matrixes to obtain a comprehensive similarity matrix fusing all information, obtaining an adjacent matrix, constructing a network diagram, and performing community division on the network diagram by using a louvain algorithm; combining the feature sequences in each community by using a DOA method to obtain a representative sequence of each community; and summarizing the representative sequences of the communities by using a DOA method to obtain a final sequence based on the fusion similarity matrix. According to the invention, a more comprehensive screening result is obtained based on results of different feature screening methods.

The application discloses a primer design method, system and computer storage medium based on minimum degeneracy, the method comprising: obtaining nucleotide sequences; dividing the nucleotide sequences into multiple classification units; selecting a representative sequence from each classification unit; designing a corresponding primer pair set for the representative sequence based on the base frequency in the representative sequence; determining the coverage of the primer pair set relative to all nucleotide sequences, and selecting multiple primer pairs in each primer pair set as a candidate primer pair set according to the coverage of each primer pair set; and selecting multiple candidate primers in the candidate primer pair set to establish a primer pool. The application considers the mismatch between primer pairs and the coverage in the primer design process, thereby allowing the primer pairs to have extremely high coverage and lower degeneracy.

The application discloses a high-throughput sequencing data sequence clustering method and system based on cyclic self-blast: the high-throughput sequencing data is de-duplicated; unique sequences with a number of repetitions lower than a threshold value a are filtered, and the filtered unique sequences are sorted according to the number of repetitions; the sorted unique sequences are divided into subsets and a parent set; the subsets are subjected to blast multiple alignment to obtain a de-redundant subset; the parent set and the de-redundant subset are subjected to cyclic blast alignment to obtain a de-redundant parent set; all representative sequences in a preliminary clustering set are combined, sorted according to the number of repetitions and distributed with identification tags to generate a final OTU clustering result set; in the prior art, when OTU clustering and ASV methods are used to process environmental DNA macro-barcode sequencing data, different OTU or ASV sequences are annotated to the same species, so that a large amount of redundancy still exists in the classified units after clustering, and the reliability of species analysis is improved.

The invention discloses a protein sequence design method based on biomolecular interaction structural domain enhancement. The method comprises the following steps: firstly, inputting three-dimensional coordinate information of a protein main chain skeleton to be subjected to sequence design, wherein the size of the protein main chain skeleton is L * N * 3; obtaining a protein sequence in contact with the biomolecules and an interaction structural domain interval; clustering the obtained sequences and taking out a representative sequence of each cluster as a training set; extracting a three-dimensional structure, a secondary structure, solvent accessibility and function annotation feature representation of each training sample; fine-tuning the last ten layers of transformer modules of the universal multi-modal protein language model ESM3 by using an LoRA algorithm, and giving a larger weight for the loss of mask residues located in an interaction structural domain interval; and inputting atomic coordinates of a protein main chain skeleton to be subjected to sequence design into the trained model to obtain a target sequence. On one hand, multi-modal information of massive proteins is utilized; on the other hand, a more robust and reasonable functional protein sequence can be generated.

The invention discloses a high-throughput sequencing data sequence clustering method and system based on circulating self-blast. The method comprises the following steps: carrying out duplicate removal processing on high-throughput sequencing data; filtering the unique sequences of which the repetition number is lower than a threshold value a, and sorting the filtered unique sequences according to the repetition number; dividing the sorted unique sequence into a subset and a mother set; performing blast multiple comparison on the subsets to obtain redundancy-removed subsets; performing cyclic blast comparison on the mother set and the redundancy-removed subset to obtain a redundancy-removed mother set; combining all representative sequences in the preliminary clustering set, sorting according to the number of repetitions and distributing identification labels, and generating a final OTU clustering result set; in the prior art, when an OTU clustering method and an ASV method are used for processing environment DNA macro bar code sequencing data, different OTU or ASV sequences are annotated to the same species, so that a large amount of redundancy still exists in a classified unit after clustering, and the reliability of species analysis is improved.

The present invention relates to the field of biopharmaceutical technology, and discloses a method, device, computing device and storage medium for messenger ribonucleic acid sequence design. Based on a given 5' UTR sequence as the starting input, the method adds new codons one by one using the growth method, and calculates and scores the full-length minimum free energy and codon usage efficiency of the overall sequence for sorting. The elimination method is used to exclude sequences containing restriction enzyme sites / undesirable properties / or poor scores, and then the clustering search method is used to select representative sequences to increase diversity, and finally the sequences are obtained for recommended synthesis. The present invention proposes an mRNA sequence optimization design method in the environment of 5' UTR and 3' UTR, taking into account the full-length minimum free energy of the mRNA sequence and the codon usage efficiency of the CDS region, which can optimize these two objectives simultaneously, can optimize its stability from the perspective of the overall molecule, and at the same time optimize the expressibility of the CDS region, ensuring the stability and expressibility of the mRNA sequence.

This classification method comprises: a measurement step for measuring the nucleotide sequence of a nucleic acid molecule in a measurement sample as a measurement sequence; and a classification step for classifying the measurement sequence into each of a plurality of groups on the basis of the degree of similarity between a representative sequence set as a base sequence representing each of the groups and the measurement sequence measured in the measurement step. The plurality of groups are obtained by grouping the base sequences of a plurality of nucleic acid molecules according to a specific rule.

Immunological entity sequences are clustered by a two-step process based on their similarity, i.e., their ability to react to the same antigen. In the first step, the sequences are converted into numerical vectors, and these numerical vectors are clustered into initial clusters. In the second step, the initial clusters are refined into final clusters, which can be done using the sequence data itself rather than numerical vectors. Each final cluster may be assigned a representative sequence to reduce the dimensionality of the cluster.

The invention belongs to the technical field of bioinformatics, and discloses a generic genome database and a construction method and system thereof. According to the method, microorganisms or parasites provided by a plurality of public databases and / or own databases are classified, genome sequences of the microorganisms or parasites are screened out by using different screening methods, the genome sequences are further cleaned to remove polluted sequences, and finally representative sequences are screened out from the cleaned genome sequences, so that the microorganisms or parasites are screened out. And summarizing all representative sequences to complete the construction of the generic genome database. According to the generic genome database constructed by the method, the accuracy and efficiency of metagenome sequencing are remarkably improved, and the method is suitable for rapid identification of clinical infection pathogens.

The application discloses a protein sequence design method based on biomolecular interaction domain enhancement, which comprises the following steps: inputting a protein main chain skeleton three-dimensional coordinate information of a size of L*N*3 to be subjected to sequence design; obtaining a protein sequence in contact with a biomolecule and an interaction domain interval; clustering the obtained sequence and taking a representative sequence of each cluster as a training set; extracting three-dimensional structure, secondary structure, solvent accessibility and functional annotation feature representation of each training sample; using a LoRA algorithm to fine-tune the last ten transformer modules of a general multi-modal protein language model ESM3, and giving greater weight to the loss of a mask residue located in the interaction domain interval; and inputting the atomic coordinates of the protein main chain skeleton to be subjected to sequence design into the trained model to obtain a target sequence. On the one hand, the application utilizes multi-modal information of a large amount of proteins; and on the other hand, the application can generate a more robust and reasonable functional protein sequence.

To provide a method for generating a camelid antibody specific for an antigen.SOLUTION: The present invention provides a method comprising: a) enriching and proliferating B-cells from immunized camelids specific to an antigen; b) generating antibody NGS libraries comprising VHH2, VHH3, and VH1 chain sequences from the antigen-specific B-cells; c) grouping antibody sequences of VHH2, VHH3, and VH1 chain in the NGS libraries by lineages; d) ranking the lineages from step c) by one or more lineage priority factors; e) selecting a representative sequence from a lineage comprising a VHH2 or VHH3 with a top ranking from step d) in the NGS library; and f) testing an antibody comprising the selected sequence from step e) to determine if the antibody binds to the antigen or a portion thereof.SELECTED DRAWING: None