20 results about "De novo sequencing" patented technology

Example systems and methods for de novo sequencing of DNA or DNA-like sequences using Viterbi-like correlation analysis are described. A sequencing system receives the read data for multiple copies of a DNA strand from a sequence reader, such as a nanopore reader. The sequencing system generates a convolutional matrix based on one copy and a reference matrix based on another copy and uses them to generate a correlation matrix. A most likely path through the correlation matrix is determined to identify and correct errors between the two copies.

Some embodiments of the methods and compositions provided herein relate to nanopore sequencing of a target polypeptide. In some embodiments, a sequencing substrate is prepared by Edman degradation from a target polypeptide immobilized on a substrate. De novo sequencing is performed with the sequence substrate and a nanopore embedded in a membrane.

This invention belongs to the field of protein sequencing, specifically disclosing a novel solid-state sub-nanopore fabrication method and its application in protein sequencing. The technical solution involves: reliably and easily fabricating pores with a diameter less than 1 nm on a 5 nm thick pure silicon film; reconstructing the spatial structure of the pores in three dimensions at the atomic scale through transmission electron microscopy imaging and multilayer image simulation comparison; and then incorporating key geometric parameters into finite element multiphysics modeling to simulate the electric field distribution within the pores and calculate the conductivity of the sub-nanopores, thereby evaluating the application potential and performance of this fabrication method in protein single-molecule sequencing. The sensing region depth of this novel nanopore can be less than 1 nm, giving it an advantage over other similar nanopores in developing protein de novo sequencing technology with single-point residue specificity (kmer=1), providing a new approach for the single-point residue specificity detection of protein variants.

A first product ion mass spectrum of a nucleic acid analyzed using a CID method is received. Also, a second product ion mass spectrum of the nucleic acid analyzed using a radical-induced dissociation method is received. Peak m / z values of the first spectrum, peak m / z values of the second spectrum, and an m / z value of a precursor ion of the nucleic acid are converted to a single charge. A peak m / z value of the first spectrum is determined that differs from a peak m / z value of the second spectrum by a mass value of a structure within the nucleic acid the radical-induced dissociation method is known to not be able to dissociate and the CID method is known to be able to dissociate. The structure includes a phosphorus atom and an optionally substituted 5-membered ring containing an oxygen.

The application provides a completely humanized anti-human blood coagulation factor IX monoclonal antibody or an antigen binding fragment thereof and application thereof. The antibody provided by the application has high affinity to human blood coagulation factor IX and significant inhibitory activity, and belongs to a neutralizing antibody, and has a good treatment prospect for thrombus diseases. The functional antibody is directly screened from blood plasma of hemophilia B patients by a mass spectrometry + de novo sequencing technology, and has the advantages of complete human origin, high safety and the like.

This invention discloses a nanopore peptide sequencing method based on host-guest interactions. The method includes the following steps: 1) sequentially hydrolyzing the peptide to be sequenced into monomeric amino acids using a proteolytic enzyme; 2) linking the monomeric amino acids to a load molecule containing the guest molecule structure; 3) performing single-channel recording in a nanopore after the host molecule and guest molecule have bound. This invention provides a de novo sequencing method that utilizes the sequential hydrolysis of peptides by exopeptidases to obtain the peptide sequence information; by linking the load molecule to a single amino acid, the current blocking ratio of the characteristic signals generated after the binding of 20 encoding amino acids to the load molecule is accurately measured. The characteristic current is contributed by a single amino acid, eliminating decoding difficulties; the target peptide dosage is small, and the detection limit is low; the experimental operation is safe and simple, with most reactions carried out in an aqueous phase, without involving toxic reagents, making it green and safe.

The invention provides a protein database searching and de novo sequencing model and a training method thereof, the model comprises a peptide fragment sequence encoder, a mass spectrogram encoder, a combined modal scoring device and a peptide fragment length sensing decoder, the method comprises the steps of utilizing a training set to train the model for multiple rounds, and each sample comprises mass spectrogram data and a real peptide fragment sequence. Searching a candidate peptide fragment set according to mass spectrum data in each round; encoding each peptide fragment sequence in the set by using a peptide fragment sequence encoder to obtain each peptide fragment feature representation, and encoding the mass spectrum data by using a mass spectrum encoder to obtain a mass spectrum feature representation; aiming at a search task, processing the characteristic representation of the mass spectrum and the characteristic representation of each peptide fragment by utilizing a combined modal scoring device to obtain a matching score of each peptide fragment sequence and the mass spectrum data; aiming at a de novo sequencing task, generating a peptide fragment sequence by utilizing a peptide fragment length sensing decoder according to mass spectrum characteristic representation; and constructing a total loss function based on the two tasks to update model parameters.

Computerized methods and systems of de novo sequencing from a mass spectrometer and identifying a biological polymer using mass invariant charge patterns in the spectrometer data by transforming spectra to a natural logarithmic space where peaks arising from the same analyte mass align along a predictable pattern defined solely by charge state. In some embodiments, the computerized method employs an operation that iterates the residue mass in the transformed natural logarithmic space, e.g., minimizing charge state difference errors between corresponding isotopologues assigned to different charge states. In some embodiments, the de novo sequencing of the present disclosure also allows for viewing the mass-to-charge (m / z) spectrum in a natural logarithmic manner (e.g., Equation 1—ln(m / z−q)) to provide confidence in any reassignment of peaks in an observed charge pattern vector.

The invention relates to a de novo sequencing method for rapidly and simultaneously identifying amino acid sequences of mixed antibodies, in the method, most abundant peptide fragment information can be provided for identification or analysis of the amino acid sequences of the antibodies through a gradient enzymolysis strategy, and further, the amino acid sequences of the antibodies can be identified and analyzed. A more efficient, higher-throughput, economical and practical de novo sequencing method is provided for accurate and complete de novo sequencing of the mixed antibody, and the method is particularly suitable for rapid research and development of the antibody and has a very wide application prospect.

Example systems and methods for de novo sequencing of DNA or DNA-like sequences using Viterbi-like correlation analysis are described. A sequencing system receives the read data for multiple copies of a DNA strand from a sequence reader, such as a nanopore reader. The sequencing system generates a convolutional matrix based on one copy and a reference matrix based on another copy and uses them to generate a correlation matrix. A most likely path through the correlation matrix is determined to identify and correct errors between the two copies.

The invention provides a completely humanized anti-human coagulation factor IX monoclonal antibody or an antigen binding fragment thereof and application thereof. The antibody provided by the invention has high affinity and remarkable inhibitory activity on the human coagulation factor IX, belongs to a neutralizing antibody, and has a good treatment prospect on thrombosis diseases. The functional antibody is directly screened from the blood plasma of the hemophilia B patient through the'mass spectrum + de novo sequencing 'technology, and the method has the advantages of being completely humanized, high in safety and the like.

The invention relates to a polypeptide for treating Alzheimer's disease (AD) and a preparation method thereof, and belongs to the field of biological medicine and natural product development. The method comprises the following steps: carrying out enzymolysis on sea cucumber intestine protein, separating low-molecular-weight polypeptide, carrying out de novo sequencing and carrying out high-throughput polypeptide synthesis, and screening and verifying polypeptides LSPGV (leucine-serine-proline-glycine-valine) and YPGQLT (tyrosine-proline-glycine-glutamine-leucine-threonine) which have antioxidant activity and acetylcholin esterase (AChE) inhibition activity. In-vitro experiment results show that the polypeptide can significantly remove DPPH free radicals and inhibit AChE activity. A nematode in-vivo experiment further verifies that the compound can effectively delay an A beta-induced paralysis process and reduce AChE activity and A beta aggregation level, and shows good anti-AD potential. The invention provides an efficient screening method for the development of the anti-AD active peptide from a natural source, and provides a new bioactive molecule for the prevention and treatment of AD.

The invention provides a mass spectrum data analysis method of a new N-terminal protein variant, which breaks through the limitations of proteogenomics and de novo sequencing. A first specific property spectrum data analysis algorithm NovelNSeq specially aiming at a marker peptide fragment (a new N-terminal extension peptide fragment) of a new N-terminal protein is developed, and the algorithm does not depend on transcriptome data or de novo sequencing. By fully utilizing the peptide fragment coding logic, the accuracy is obviously higher than that of a mainstream de novo sequencing algorithm, and the method has the traceability of a peptide fragment coding mechanism. A plurality of new N-terminal protein variants coded by human genes are identified and verified in deep coverage mass spectrum data, the variants are not found in large-scale proteogenomics research of the same mass spectrum data, and NovelNSeq is proved to be capable of serving as an important supplement of a traditional method and is a powerful tool for finding new N-terminal proteins.

The invention is applicable to the technical field of biological analysis, and provides a mass spectrum-based monoclonal antibody IgM de novo sequencing method which comprises the following steps: providing a monoclonal antibody IgM sample; carrying out reduction and alkylation treatment on the sample; carrying out enzymolysis on the treated sample by using specific endoprotease; analyzing by adopting a liquid chromatography-mass spectrometry technology to obtain mass spectrometry data; the mass spectrum data is subjected to de novo analysis through a data processing algorithm, and the amino acid sequence of the monoclonal antibody IgM is deduced. By means of the optimized sample pretreatment process, the quality and stability of a peptide fragment product are remarkably improved; a high-resolution mass spectrum platform and an innovative SIM-DIA acquisition mode are adopted, so that more comprehensive and more accurate mass spectrum data are obtained, and particularly, the detection rate of low-abundance peptide fragments is increased; through independently researched and developed data analysis software and algorithm, efficient and accurate analysis of complex mass spectrum data is realized, and the efficiency and success rate of de novo sequencing are greatly improved.

The invention belongs to the technical field of biological analysis, and relates to an antibody sequencing method and device, in particular to an antibody peptide sequence assembling method and device based on beam search. Specifically, the invention relates to an antibody sequencing method which comprises the following steps: S1, obtaining a homologous template of an antibody to be detected; s2, cleaning the de novo sequencing data of the peptide fragment to obtain a cleaned peptide fragment sequence; s3, segmenting the cleaned peptide fragment sequence into a short peptide sequence with a fixed length; and S4, based on the amino acid information on the homologous template and the signal intensity of the oligopeptide sequence, constructing a Debrueine map through beam search, and carrying out sequence assembly to obtain an antibody sequence. The flux of the monoclonal antibody from the beginning sequencing can be improved, so that the mass spectrometric detection time and the cost of experimental consumables are reduced, and the method has a good application prospect.

The application discloses a CNV marker of WNT2B gene of intersex pigs and application, the marker is located in the WNT2B gene, and the gene candidate region is chr-4:107914901-107923000, and the application is used for pig breeding through the CNV marker of WNT2B gene.The 10xGenomics de novo sequencing technology is adopted in the application, and the sequencing depth reaches 60x, so that more than 99% of genome coverage is realized;the pathogenic gene causing 38, XX-DSD pig gender development abnormalities can be more accurately found.The distribution of the CNV in a pig population is detected in the application, and the ATAC-seq and RNA-seq sequencing technologies are also adopted, so that the reliability of the WNT2B gene CNV marker is verified from the chromatin accessibility and the expression amount of transcripts.

The invention relates to a method for identifying nucleic acid modification in a to-be-detected RNA (Ribonucleic Acid) sequence, which comprises the following steps of: performing molecular weight detection on a complete to-be-detected RNA sequence and actual enzyme digestion fragments of single enzyme digestion and double enzyme digestion; and carrying out molecular weight comparison with a theoretical enzyme digestion fragment obtained by carrying out theoretical enzyme digestion of the same enzyme on a theoretical sequence which does not contain ribose and / or basic group modification or contains part of ribose and / or basic group modification, so as to obtain a modification mode of ribose and / or basic group in the RNA sequence to be detected. According to the information, the specific variety, quantity and position of ribose and / or base modification in the RNA sequence to be detected can be uniquely determined, or a possible ribose and / or base modification mode in the RNA sequence to be detected is limited in a limited range; therefore, the specific variety, quantity and position of ribose and / or base modification in the RNA sequence to be detected can be easily obtained through subsequent analysis.

Computerized methods and systems of de novo sequencing from a mass spectrometer and identifying a biological polymer using mass invariant charge patterns in the spectrometer data by transforming spectra to a natural logarithmic space where peaks arising from the same analyte mass align along a predictable pattern defined solely by charge state. In some embodiments, the computerized method employs an operation that iterates the residue mass in the transformed natural logarithmic space, e.g., minimizing charge state difference errors between corresponding isotopologues assigned to different charge states. In some embodiments, the de novo sequencing of the present disclosure also allows for viewing the mass-to-charge (m / z) spectrum in a natural logarithmic manner (e.g., Equation 1 - ln (m / z-q)) to provide confidence in any reassignment of peaks in an observed charge pattern vector.

Computerized methods and systems of de novo sequencing from a mass spectrometer and identifying a biological polymer using mass invariant charge patterns in the spectrometer data by transforming spectra to a natural logarithmic space where peaks arising from the same analyte mass align along a predictable pattern defined solely by charge state. In some embodiments, the computerized method employs an operation that iterates the residue mass in the transformed natural logarithmic space, e.g., minimizing charge state difference errors between corresponding isotopologues assigned to different charge states. In some embodiments, the de novo sequencing of the present disclosure also allows for viewing the mass-to-charge (m / z) spectrum in a natural logarithmic manner (e.g., Equation 1 −ln(m / z−q)) to provide confidence in any reassignment of peaks in an observed charge pattern vector.