Index acceleration method and corresponding system in scale protein identification

Abstract

The invention provides an index acceleration method in scale protein identification, which comprises the following steps of: setting quality intervals for peptide sequences; setting the size of counting windows, and setting the number of the counting windows and the range of each counting window by combining the quality intervals; performing simulated enzyme digestion on protein database, and calculating the quantity of the peptide sequences in each counting window according to the quality of the peptide sequences obtained through the simulated enzyme digestion; obtaining the quantity of the peptide sequences which can be processed once in the memory of a computer according to the capacity of the memory of the computer, and obtaining a quality range section of the peptide sequences which can be processed once in the memory of the computer by combining the quantity of the peptide sequences in each counting window; performing the simulated enzyme digestion on the protein database, saving the obtained peptide sequences in one quality range section in the memory of the computer, and finishing the operations of sequencing, redundancy removal, and dictionary and inverted list establishment on the saved peptide sequences in the memory of the computer; and establishing a dictionary and an inverted list for each quality range section.

Description

technical field [0001] The invention relates to an accelerating method for large-scale protein identification, in particular to a method for improving protein identification speed by adopting an inverted index to reorganize a protein database. Background technique [0002] The term "Proteome" was first proposed by Wilkins et al. in 1997 to describe the protein counterpart of the genome. The proteome depicts the ensemble of proteins expressed at a given moment and under given conditions in a particular biological sample. As the name suggests, proteomics is the study of the proteome. Its most basic task is to determine which proteins are expressed in the organism, how much they are expressed, post-translational modifications, and protein-protein interactions, etc., thereby obtaining protein levels. A holistic and comprehensive understanding of disease occurrence, cell metabolism and other processes in the world. In current proteome research, protein identification based on t...

AI Technical Summary

Problems solved by technology

However, this method still has large defects in time and space performance.

First of all, the division method of temporary files is unreasonable. For protein databases with different characteristics, this method may lead to uneven distribution of peptide sequences in ten temporary files; secondly, this method involves a large number of file operations. Files need to be sorted in external storage

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