The present disclosure provides methods of identifying and quantifying the peptides displayed by the major histocompatibility complex (MHC). Such methods may comprise the ability to determine the type, identity, and quantity of each peptide displayed by the MHC. In some embodiments, these methods may be used to develop an anti-cancer therapy or type the HLA of a patient. Also provided herein are compositions comprising peptides from the MHC which have been prepared for sequencing.

The present systems and methods introduce deep learning to de novo peptide sequencing from tandem mass spectrometry data. The systems and methods achieve improvements in sequencing accuracy over existing systems and methods and enables complete assembly of novel protein sequences without assisting databases. The present systems and methods are re-trainable to adapt to new sources of data and provides a complete end-to-end training and prediction solution, which is advantageous given the growing massive amount of data. The systems and methods combine deep learning and dynamic programming to solve optimization problems.

The present systems and methods introduce deep learning to de novo peptide sequencing from tandem mass spectrometry data. The systems and methods achieve improvements in sequencing accuracy over existing systems and methods and enables complete assembly of novel protein sequences without assisting databases. The present systems and methods are re-trainable to adapt to new sources of data and provides a complete end-to-end training and prediction solution, which is advantageous given the growing massive amount of data. The systems and methods combine deep learning and dynamic programming to solve optimization problems.

Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

The invention provide an assessment method and device for infectious disease transmission, computer equipment and storage medium. The method comprises: obtaining respective target track data corresponding to assessment objects within a preset area in a first time slice; determining a matching subarea to which each assessment object matches in the first time slice based on the target track data; taking at least one of the plurality of subareas as a target subarea, and assessing an assessment object within the target subarea based on an infectious disease model to determine a transmission trend of an infectious disease for the assessment object within the preset area in the first time slice; and taking a next time slice as the first time slice, and re-performing the above steps until end of the target time period to determine a transmission trend of the infectious disease among the assessment objects during the target time period.

The invention provide an assessment method and device for infectious disease transmission, computer equipment and storage medium. The method comprises: obtaining respective target track data corresponding to assessment objects within a preset area in a first time slice; determining a matching subarea to which each assessment object matches in the first time slice based on the target track data; taking at least one of the plurality of subareas as a target subarea, and assessing an assessment object within the target subarea based on an infectious disease model to determine a transmission trend of an infectious disease for the assessment object within the preset area in the first time slice; and taking a next time slice as the first time slice, and re-performing the above steps until end of the target time period to determine a transmission trend of the infectious disease among the assessment objects during the target time period.

A method for information encoding and decoding, and method for information storage and interpretation are provided. The information encoding method includes: first binary information and second binary information as well as a first encoding rule and a second encoding rule are obtained; a first output candidate symbol corresponding to a current input of the first binary information is obtained and a second output candidate symbol corresponding to a current input of the second binary information is obtained, and an intersection of the first output candidate symbol and the second output candidate symbol is taken as an output corresponding to a current input; and an output symbol corresponding to each binary bit of the first binary information and the second binary information is sequentially determined through the first encoding rule and the second encoding rule, as to obtain an encoding sequence formed by a plurality of the output symbols.

A meter value that reflects the amount of genetic material stored in a reserve is stored in a database for each reserve in a bank. Meter values allow a user to track the amount of genetic material in the reserves of a bank without needing to physically measure or disturb the reserves unnecessarily. As users withdraw and deposit genetic material from and into a reserve, the meter value is changed to reflect the change in the amount of genetic material in the reserve. In certain embodiments, the use of meter values enables accurate and instant accounting of a large number of reserves of genetic material for a large number of individuals. Users and/or individuals may be notified when a meter value falls below a threshold. Notifications may prompt a user to generate additional genetic material from biological sample or an individual to provide additional biological sample.

The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.