35 results about "Protein database" patented technology

The invention provides a method and a device for detecting mutated proteins. The method includes acquiring transcriptome data corresponding to samples; comparing the transcriptome data to mitochondrion databases and outputting non-mitochondrion sequences according to comparison results of the transcriptome data and the mitochondrion databases; transforming nucleotide sequences in the non-mitochondrion sequences into amino acid sequences, comparing the transformed amino acid sequences to protein databases and extracting amino acid sequences with homogenous rates in first set ranges and amino acid lengths in second set ranges from comparison results of the transformed amino acid sequences and the protein databases; comparing the extracted amino acid sequences with the homogenous rates in the first set ranges and the amino acid lengths in the second set ranges to NCBI (national center of biotechnology information) and determining the mutated proteins according to comparison results of the extracted amino acid sequences and the NCBI. According to the scheme, the method and the device have the advantage that the mutated proteins in the samples can be detected by the aid of the method and the device.

The invention discloses a drug target interaction prediction method based on multilayer network representation learning, and mainly solves the problem of low prediction accuracy in the prior art. Themethod comprises the following steps: downloading data from a drug and protein database, and respectively constructing multilayer similarity networks of drugs and proteins; calculating diffusion states of the two similarity networks respectively, and integrating the diffusion states respectively to obtain feature vectors of drugs and proteins; taking known drug target interaction data as supervision information, putting the drug and protein feature vectors into the same drug target space, and respectively obtaining projection matrixes of the drug and the protein by using a bilinear function; obtaining a prediction score matrix of drug target interaction according to the two projection matrixes and ranking the prediction score matrix; regarding eight top-ranked unknown drug target pairs aspotential drug target interactions. According to the method, the prediction accuracy of drug target interaction is improved, and the method can be used for predicting candidates of drug target pairs.

The invention discloses a DNA binding protein identification and function annotation deep learning method based on a self-attention mechanism. The method comprises the following steps: selecting a data set from a protein database, training and testing a constructed deep learning model by using the selected data set, and predicting whether protein can be combined with DNA by using the trained deeplearning model, wherein the deep learning model comprises a coding layer, an embedding layer, a long short-term memory neural network layer (LSTM), a convolutional neural network layer (CNN) and a self-attention layer (Self-Attention). Through a deep learning model based on a self-attention mechanism, whether the protein has a function of combining with DNA or not can be predicted according to primary sequence information of the protein, and an area with a combining function is found out.

The invention provides a lathyrus quinquenervius EST-SSR primer group developed based on transcriptome sequencing, a method and application. The method comprises the steps of obtaining a set of all root, stem and leaf transcripts of two lathyrus quinquenervius varieties of different flower colors at a seedling stage to form an original sequence database; removing low-quality sequencing data with a joint and forming a high-quality filtered sequence database; splicing high-quality filtered sequences, reducing the transcripts and carrying out BLAST comparison on the transcripts and a reference protein database NR, reserving the optimal comparison result and determining the maximal sequence as a Unigene representative sequence; carrying out SSR locus scanning in Unigene by using MISA 1.0; and carrying out SSR primer design by adopting primer 3.0, screening SSR primers and carrying out fingerprint map construction on 43 parts of lathyrus quinquenervius materials. The lathyrus quinquenervius EST-SSR primer group is convenient, fast, accurate, low in cost, and a new thought is provided for the development of lathyrus quinquenervius EST-SSR primers and germplasm resources identification.

The invention discloses a bioinformatics method for constructing an antibiotic resistance genbank in the biotechnology field. The method comprises the following steps that: searching the protein sequence of a resistance gene in a GenBank; selecting a sequence with high accuracy as an initial sequence; adopting a Clustalw method for comparison; constructing a hidden Markov model, and searching a GenBank protein database to obtain all sequences which contain protein conserved sites; according to the E values of the sequences and the annotation information of the sequences in the GenBank database, removing the sequences which are highly homologous and do not conform to requirements; and after repeated sequences are removed, adding species annotation information; and integrating all protein sequences to finish database construction. By use of the method, the annotation information and the comparison similarity of a sequence can be comprehensively measured, and sequence collection speed andaccuracy can be improved. By use of the method provided by the invention, the construction of the antibiotic resistance genbank can be finished, and a basic data is provided for researching the primer design, the data analysis and the sequence annotation of the resistance gene.

The invention discloses a template-based multi-domain protein structure assembling method. The method comprises the steps of firstly, comparing domain proteins once by utilizing a protein structure comparison tool TM-align according to the structures of the domain proteins, and finding out an optimal template from a multi-domain protein database; secondly, obtaining a rotation and translation matrix by utilizing a Kabsch method, overlapping the domain proteins to the template, and performing translation and rotation operations on the domain proteins, thereby enabling a distance between the domain proteins to be equal to a minimum allowed distance; thirdly, performing adjustment by performing random translation and rotation on an assembled structure, and measuring the quality of the assembled structure by utilizing a conflict factor between the domain proteins, an interactive atom quantity and a moving range of the assembled structure relative to the template; and in an assembling process, assembling the adjacent domain proteins in sequence, fixing the assembled structures, and when all the structures are assembled, outputting a final assembling result. The template-based multi-domain protein structure assembling method provided by the invention is relatively high in prediction precision.

The invention discloses a compression and clustering-based batch protein homology search method and belongs to the cross field of computer application technologies and bio-technologies. The method comprises the steps of firstly performing compression operation on a query sequence and a protein database through redundancy analysis and redundancy removal processes by fully utilizing sequence similar information existent in a protein database sequence and the query sequence; secondly performing similar sub-sequence clustering on the compressed protein database; thirdly performing a search by utilizing a mapping principle based on the clustered database to discover potential results, and establishing an executable database according to the found potential result set; and finally performing a homology search in the executable database to obtain a final homology sequence. According to the method, the homology search is performed in the established executable database, so that the time for repeated sequence comparison and gapless expansion is greatly shortened.

The present invention designs a method for using literature mining technology to study the relationship between virus and human protein expression regulation, including the following main steps: step 1, predicting the direct target gene from microRNA; step 2, predicting the direct target protein from the above target gene; Step 3, use literature mining technology to construct a protein-protein interaction database; Step 4, use the constructed protein interaction database to screen out the indirect target protein and indirect target gene of microRNA from the direct target protein; Step 5, through the experiment Validation of indirect target genes of microRNAs. The feature of this method is that an "indirect" target gene model is proposed, and the literature mining technology is introduced to screen out the real microRNA target genes that are difficult to detect by conventional methods.

The invention relates to a disease-related protein database, a construction method and an application thereof. The database has the characteristics of extensive data collection of disease-related proteins, timely updating, including structural information, no local installation and fast access. At the same time, the construction method of the disease-related protein database and its application inscientific research are provided.

The invention obtains the specific expression protein of wheat salt tolerant mutant, and finds by mass spectrum identification, Web protein database search and bio-information technique that the protein has high homology with one assumed protein on the 4th rice chromosome. Accordingly, it designs primer, amplifies by PCR to obtain the corresponding wheat salt tolerance gene with 153 amino acids and 462bp length; clones the gene to construct pronucleus expression vector to express out a specific protein with molecular weight as 16.8KD and improve the salt tolerance of escherichia coli obviously. This invention settles foundation for wheat salt tolerance mechanism.

A method for identifying microorganisms by MALDI-TOF mass spectrometry includes acquiring a MALDI mass spectrum of a microorganism, detecting peaks in the acquired MALDI spectrum, generating a peak list comprising mass and intensity from the detected peaks in the acquired MALDI spectrum, acquiring a database of protein sequences deduced from DNA sequences for microorganisms, generating a sub-database of ribosomal proteins from the protein sequences and their masses in the database, matching masses of the detected peaks in the acquired MALDI spectrum to masses of the ribosomal proteins in the generated sub-database, scoring the matches obtained above for each represented microorganism, generating a peak list of accurate masses of matched ribosomal proteins, recalibrating the peak list comprising mass and intensity with the peak list of accurate masses of matched ribosomal proteins, identifying a microorganism with the highest score, and repeating until a desired improvement in the recalibrated peak list or a validated identification is achieved.

The invention discloses a destructive beta-conglycinin beta subunit processing antigen area and a screening method based on phage display technological orientation. The amino acid sequence of the antigen area is as shown in SEQ ID NO. 15. By the aid of a series of bioinformatics software and reference of an analyzed beta-conglycinin three-dimensional crystalline structure of a PDB (protein database), the antigen area of ultrahigh-pressure destructive beta-conglycinin is researched by a phage display technology, a beta-conglycinin beta subunit and overlapping protein thereof are represented onthe surface of a phage, and an area with the beta-conglycinin beta subunit with antigenicity reduced by an ultrahigh-pressure is accurately positioned. A theoretical basis for screening processing methods is provided for food industry, and an application product for rapidly detecting the desensitization effect of processed food can be further developed.

The invention discloses a method for analyzing the transcription and translation activity of functional genes of a microbial community. The method comprises the following steps: extracting a total DNAsample, total RNA sample and total protein sample of the microbial community; carrying out metagenome sequencing, metatranscriptome sequencing and meta-protrinology analysis on the extracted samples;constructing a microbial community functional gene coded protein database by utilizing a metagenome sequencing result; analyzing the transcription activity of the functional genes of the microbial community on the basis of the protein database and an mRNA sequence data set generated by metatranscriptome sequencing; and analyzing the translation activity of the functional genes of the microbial community on the basis of a meta-protrinology analysis result and the protein database. According to the method, the unified microbial community functional genome protein database is constructed, and the expression quantities of transcription and translation of the functional genes of the community are analyzed according to the database; the differences of the expression levels of transcription andtranslation of the functional genes of the community are directly compared, thereby researching the post-transcriptional control process of the functional genes of the community.

An unidentified purified protein can be uniquely identified by combining one or more physical parameters of the protein and an accurate amino acid content. The protein can be identified by input of the one or more physical parameters and the amino acid content into an interface that outputs data from a protein database.

The invention relates to a random forest-based sucrose transporter identification method, which comprises the following steps of: firstly, acquiring initial data from a protein database, preprocessing the initial data, deleting sequences containing non-standard letters and sequences with too short lengths, and deleting sequences with the similarity greater than 60%; extracting different features according to physicochemical properties and evolutionary information of the protein, and taking each feature and the combined feature as feature input; then, due to the fact that the difference between the sample numbers of the positive example and the counter example is large, performing oversampling on the data set; and finally, under ten-fold cross validation, performing feature training on the oversampled training set by using a random forest, a support vector machine, stochastic gradient descent and naive Bayes, performing testing by using a test set, and analyzing a result. According to the method, a k-separated-bigrams-PSSM and random forest combined method is used, and a Borderline-SMOTE algorithm is introduced, so that the problem of data imbalance is solved, and the identification accuracy of the sucrose transporter is effectively improved.

The invention discloses a method for screening characteristic fragments of yak collagen through high-resolution mass spectrometry. The method is characterized by comprising the following steps: (1) sample collection; (2) pretreatment; (3) performing enzymolysis; (4) high performance liquid chromatography separation: separating the enzymatic hydrolysate by adopting a high performance liquid chromatography system EasynLC with a nano-liter flow velocity; (5) mass spectrum identification: carrying out mass spectrum identification by using a Q-Exactive mass spectrometer after carrying out chromatographic separation on the enzymatic hydrolysate; and (6) characteristic fragment screening: retrieving a UniProt protein database in an original file of a mass spectrum identification result by using Mascot2.2 software, and screening to obtain the characteristic fragments of the yak collagen. According to the method, yak collagen subjected to enzymolysis is separated and identified through a high performance liquid chromatography-tandem mass spectrometry technology, data are compared and analyzed through Mascot2.2 software and a UniProt protein database, and yak collagen characteristic fragments which can be detected in an actual sample are screened out. The identified characteristic fragments can be used for detecting the authenticity and reliability of the yak-derived collagen, and an effective technical support is provided for the aspect of yak collagen component supervision.

The invention relates to a differential protein database for expressing kidney deficiency testis and a construction method thereof. The differential protein database for expressing kidney deficiency testis is obtained by selecting a mode of deficiency of kidney-yin and a mode of deficiency of kidney-yang induced by hydrocortisone and comparing differential proteins of a normal model, the mode of deficiency of kidney-yin and the mode of deficiency of kidney-yang for expressing testis by means of an iTRAQ technology, a protein interaction network and a clustering analyzing means. Essence of deficiency of the kidney is explained by means of the differential protein database constructed, and the differential protein database provides a basis for diagnosing and treating deficiency of the kidneyin the aspect of proteomics and has very important meaning in diagnosing and treating male reproductive dysfunction.