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Protein rapid detection method based on matched microalgae protein characteristics sequence label and system thereof

A protein sequence and characteristic sequence technology, applied in proteomics, sequence analysis, genomics, etc., can solve the problems of time-consuming data sets, inability to provide all sequence information, and misleading users

Inactive Publication Date: 2017-05-24
THE FIRST INST OF OCEANOGRAPHY SOA
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  • Description
  • Claims
  • Application Information

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Problems solved by technology

The search results of the existing methods only indicate the matching part of the target sequence, and cannot provide all the information of the sequence, and sometimes even give ambiguous results, which mislead users, and all need to be supplemented by manual search. Faced with a large number of data sets time-consuming

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  • Protein rapid detection method based on matched microalgae protein characteristics sequence label and system thereof
  • Protein rapid detection method based on matched microalgae protein characteristics sequence label and system thereof
  • Protein rapid detection method based on matched microalgae protein characteristics sequence label and system thereof

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Embodiment

[0115] For the input of characteristic enzyme parameters, take the following data as an example:

[0116] The fatty acid desaturase family is mainly composed of six desaturases, delta-4, delta-5, delta-6, delta-8, delta-9 and delta-12, and each fatty acid desaturase sequence contains multiple specific proteins feature fragment. For example, the following desaturases need to be searched:

[0117] Delta-4: HPGG, HMGGH, HNKHH, QIEHH

[0118] Delta-5: HPGG, HEGGH, HNKHH, QIEHH

[0119] Delta-6: HDTLH, HNLHH, QIEHH

[0120] Delta-8: HPGG, HDYLH, HNTHH, QTEHH

[0121] Delta-9: HRTHH, HNWHH

[0122] Delta-12: HECGH, HAKHH, HVVHH

[0123] i∈1-15, the protein characteristic value fragment (Protein Character Fragment) j is defined as:

[0124] PCFi∈[HRTHH,HNWHH,HPGG,HEGGH,HNKHH,QIEHH,DHTLH,HNLHH,HECGH,HAKHH,HVVHH,HDYLH,HNTHH,QTEHH,HMGGH]

[0125] For step 1, the obtained text files to be retrieved are often hundreds of megabytes or even several gigabytes. To find delta sequences...

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Abstract

The invention discloses a protein rapid detection method based on a matched microalgae protein characteristics sequence label and a system thereof; the method includes steps of collecting a microalgae sample, and acquiring its protein sequence set, converting it to a standard protein sequence set, performing splitting and configuration treatment, and converting the protein sequence set to a key / value pair list specific to a given sequence segment; after summarizing the key / value pair list, performing an intersection operation; when the result is not empty, confirming that one data of the data set contains the characteristic protein sequence. The system mainly includes a detection data input module, a key / value pair list module, a detection identification module, a characteristic value intersection operation module, and an output module. Through indexing the protein sequence, the method and the system judge the protein homology and similarity level; by comparing with the traditional method of comparing data one by one, the algorithmic identification accuracy is and efficiency are significantly improved, the indexing efficiency is greatly promoted; the method and system have good practicability, and the algorithmic time complexity is low, the performance is high; therefore, the method and the system are significant to study proteomics.

Description

technical field [0001] The invention belongs to the technical field of microalgae gene development and utilization, in particular to a protein detection method and system based on microalgae protein characteristic sequence tag matching. Background technique [0002] Marine microalgae are the main primary producers in water ecosystems, accounting for 40.86% of marine species. They have small size, large quantity, simple cell structure, short growth cycle, large biomass, high photosynthetic efficiency, strong adaptability, and Restricted by climate, easy to cultivate and other advantages, it has attracted widespread attention. Microalgal unsaturated fatty acids contained in microalgae have the functions of maintaining the structure and function of biofilm, regulating ion channels, regulating gene expression, and participating in active substances. Synthesis, prevention and treatment of cardiovascular diseases, regulation of immune system functions and other physiological funct...

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Application Information

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IPC IPC(8): G06F19/18G06F19/22
CPCG16B20/00G16B30/00
Inventor 王帅郑立陈军辉
Owner THE FIRST INST OF OCEANOGRAPHY SOA
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