Bioinformatics method based on protein mass spectrum data annotation eukaryote genome

Abstract

The invention discloses a bioinformatics method based on a protein mass spectrum data annotation eukaryote genome. The method specifically comprises the steps of 1, constructing a high-coverage eukaryote multi-omics sequence database; 2, removing eukaryotic protein sequence database redundancy; 3, conducting mass spectrum original data format conversion; 4, adopting a database searching engine with different algorithms, and retrieving mass spectrum data separately; 5, conducting peptide fragment spectrum matching and scoring on a retrieved and processed result; 6, screening result data after type FDR system evaluation; 7, verifying an annotated encoding gene; 8, authenticating a new gene which is not annotated; 9, authenticating alternative splicing; 10, authenticating functional point mutation; 11, aiming at protein posttranslational modification, conducting large-scale authentication; 12, conducting functional annotation of the new gene and the posttranslational modification. According to the bioinformatics method based on the protein mass spectrum data annotation eukaryote genome, the accuracy and sensitivity of protein mass spectrum data analysis are comprehensively improved, in-depth analysis and annotation for the eukaryote genome is achieved, and the method specifically has the advantages of being efficient, accurate and comprehensive.

Description

technical field [0001] The invention belongs to the field of bioinformatics, and in particular relates to a bioinformatics method for annotating eukaryotic genomes based on protein mass spectrum data. Background technique [0002] Genome sequencing can only measure the base pair sequence of the entire DNA, but cannot directly measure the genes and their functions on the DNA. The sequence must be analyzed through bioinformatics methods, combined with proteomics and transcriptomics , to mine and annotate genes and their functions, which is called gene annotation. [0003] Genome annotation is a high-throughput annotation of the biological functions of all genes in the genome using bioinformatics methods and tools, and is a hot spot in current functional genomics research. [0004] The prediction of gene structure is of great significance for discovering new genes and understanding the rules of genome structure, and is an important content of various genome projects. At prese...

AI Technical Summary

Problems solved by technology

However, this method has some shortcomings: for example, due to the instability of mRNA, it is difficult to obtain the full-length mRNA sequence of some genes; in some species, the transcript encodes an operon instead of a gene; The start site is easily affected by many factors, and it is difficult to rely on mRNA to determine the start codon and stop codon

Although it can benefit from the establishment of these methods, the current research on proteomics analysis methods is still in its infancy, and its analysis methods are still computationally challenging, and there are inevitably some problems: A. Limitations of data search : Directly use the genome to construct the eukaryotic protein genome database, coupled with the rapid expansion of the search space brought about by other search conditions, it will inevitably lengthen the search time and reduce the sensitivity (number of identifications) and specificity (correctness) of mass spectrum matching. identification number)

In addition, there are still some urgent problems in this field, for example, which new splice variant fragments can be translated into stable and functional proteins? How does DNA variation data provide valuable information on proteome-level regulation?

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