Method and system for accelerating large-scale protein identification by using suffix array

A technology of protein identification and suffix array, applied in the field of suffix array to accelerate large-scale protein identification, method and system, can solve the problems of large inverted index time and space, inconvenient use, slow database search speed, etc., to improve identification Speed, less time and space, effects of reduced computation time

Active Publication Date: 2012-05-23
INST OF COMPUTING TECH CHINESE ACAD OF SCI
View PDF1 Cites 3 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0007] The purpose of the present invention is to provide a method and system for accelerating large-scale protein identification using suffix arrays, which are used to solve the slow speed of databa

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Method and system for accelerating large-scale protein identification by using suffix array
  • Method and system for accelerating large-scale protein identification by using suffix array
  • Method and system for accelerating large-scale protein identification by using suffix array

Examples

Experimental program
Comparison scheme
Effect test

Embodiment Construction

[0058] The present invention will be described in detail below in conjunction with the accompanying drawings and specific embodiments, but not as a limitation of the present invention.

[0059] Such as figure 1 Shown is a flow chart of the method for accelerating large-scale protein identification using suffix arrays in the present invention, which is mainly used in database search methods based on tandem mass spectrometry in large-scale protein identification. The concrete steps of this method process include:

[0060] Step 101, create a corresponding suffix array SA according to the protein sequence in the database, and deduce the longest common prefix LCP corresponding to the protein sequence according to SA;

[0061] Step 102, based on LCP and digestion rules, the protein sequence is digested online to obtain all non-redundant peptides;

[0062] In step 103, the peptide spectrum matching identification is carried out according to the tandem mass spectrum and the non-redu...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The invention discloses a method and a system for accelerating large-scale protein identification by using a suffix array. The method comprises the steps of: 1, establishing a corresponding suffix array according to a protein sequence in a database, and deducing a longest public prefix corresponding to the protein sequence according to the suffix array; 2, performing online enzyme digestion on the protein sequence based on the longest public prefix and an enzyme digestion rule so as to obtain a non-redundant peptide; and 3, performing peptide mapping matching identification according to a tandem mass spectrum and the non-redundant peptide, and deducing a corresponding protein sequence by utilizing the peptide obtained through identification. According to the invention, the purposes of redundant peptide removal and rapid query are achieved, and the identification speed for the protein is increased; meanwhile, the method is beneficial to lossless precision, requires less time and space and is more convenient to use.

Description

technical field [0001] The invention relates to protein identification technology, in particular to a method and system for accelerating large-scale protein identification by using suffix array (SA, SuffixArray). Background technique [0002] Protein identification based on tandem mass spectrometry has become the mainstream technology of proteomics. Reference 1 "Aebersold, R. and Mann, M. Mass spectrometry-based proteomics, Nature, 2003, 422: 198-207" has a more detailed description . And database search has become the mainstream technology for identification of tandem mass spectrometry data, reference 2 "Eng, J.K., McCormack, A.L. and Yates, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in aprotein database. J Am Soc Mass Spectrom , 1994, 5:976-989"; Reference 3 "Perkins, D.N., Pappin, D.J., Creasy, D.M.and Cottrell, J.S. Probability-basedprotein identification by searching sequence databases using mass spectrometrydata. "; ...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
IPC IPC(8): G06F19/18G06F17/30
Inventor 周郴迟浩王乐珩李由吴研洁付岩孙瑞祥贺思敏
Owner INST OF COMPUTING TECH CHINESE ACAD OF SCI
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap