Method for extracting genome gene information in batches and translating, comparing and analyzing sequences

A genome and gene technology, applied in the field of batch extraction of genome gene information and translation, comparison and analysis of sequences, can solve the problems of isolated data islands, serious data oceans, and genomic data growth

Active Publication Date: 2019-12-03
JIANGSU ACADEMY OF AGRICULTURAL SCIENCES
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0003] However, the rapid development of genomics has brought about the explosive growth of genomic data, which has led to increasingly serious problems such as data islands and data oceans.

Method used

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  • Method for extracting genome gene information in batches and translating, comparing and analyzing sequences
  • Method for extracting genome gene information in batches and translating, comparing and analyzing sequences
  • Method for extracting genome gene information in batches and translating, comparing and analyzing sequences

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0074] Example 1. Establishment of a method for efficiently extracting genomic gene information in batches and translating, comparing and analyzing sequences

[0075] The flow chart of the method for efficiently extracting genome gene information in batches and translating, comparing and analyzing sequences provided by the present invention is shown in figure 1 , including the following steps:

[0076] (1) Operate under the Linux or Window system, establish the working folder work_dir, and use the Perl script "script1.pl" according to the test transcript ID (A data set) of a certain species, follow the steps below to extract the test transcript Extract the gene ID part in front of each line from the ID and print it to the "res_Gene_ID" file (data set B) one by one.

[0077] The steps for obtaining the "res_Gene_ID" file: set up the working directory work_dir, put the script "script1.pl" and the test transcript ID file XXX1 under the working directory work_dir folder, run the...

Embodiment 2

[0131] Example 2. Use the method established in Example 1 to efficiently extract the genome information of Zhongshuang 11 rapeseed in batches and complete the translation comparison sequence analysis

[0132] Enter the oil crop genome database of the Institute of Oil Crops, Chinese Academy of Agricultural Sciences ( http: / / ocri- genomics.org / Brassia_napus_genome_ZS11 / ) Download Double 11 Brassica napus genome sequence (19 chromosomes, 976 Mb). On the Windows system or the local Linux computing server, efficiently extract the genomic information of the double 11 rapeseed and complete the translation sequence comparison calculation. During the calculation process, the commonly used program names, operating environments and addresses involved are shown in Table 1. The specific operation steps of the calculation method are as follows:

[0133] 1) Carry out with reference to the step (1) of Example 1.

[0134] Using the 271 test transcript ID files (data set A) obtained from ...

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Abstract

The invention discloses a method for extracting genome gene information in batches and translating, comparing and analyzing sequences. According to the method for extracting the genome gene information in batches and translating, comparing and analyzing the sequences provided by the invention, an MUSCLE program based on multi-sequence comparison and analysis is comprehensively applied, and a method of programming in combination with a plurality of Perl scripting languages is adopted. Experiments indicate that the method comparison system for extracting genome gene information in batches and translating, comparing and analyzing sequences can complete the extraction of a target gene sequence and a transcript sequence, acquisition of genome key information of a target gene or a transcript, DNA sequence translation and multiple comparison of a post-translation sequence, the obtained related result files are good in repetition effect and high in speed, and the batch production, automation and process are easy to achieve.

Description

technical field [0001] The invention belongs to the field of biotechnology, and relates to a method for extracting genome gene information in batches and translating, comparing and analyzing sequences. Background technique [0002] Through thousands of years of domestication and planned breeding in modern times, humans have formed today's diverse animal and crop varieties, thus providing abundant animal and plant-derived proteins to meet human needs. In the past 100 years, the application of quantitative genetics in the field of animal and plant breeding has triggered a revolution in related breeding technologies. However, the genetic development system of animals and crops is quite complex, and some traits are still difficult to efficiently select based on pedigree-based breeding values. Genetic potential has yet to be fully exploited. The ideas and technologies brought about by the Human Genome Project have greatly promoted the development of animal and plant genomics, en...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G16B20/30G16B25/10
CPCG16B30/10G16B20/30G16B25/10Y02A90/10
Inventor 郭月刘静胡茂龙浦惠明张洁夫龙卫华张维周晓婴孙程明
Owner JIANGSU ACADEMY OF AGRICULTURAL SCIENCES
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