Looking for breakthrough ideas for innovation challenges? Try Patsnap Eureka!

Method for detecting codon pair bias of bovine whole-genome

A genome-wide, assay-based technology with applications in the fields of molecular genetics and bioinformatics

Inactive Publication Date: 2012-09-26
NORTHWEST A & F UNIV
View PDF0 Cites 2 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Does the sequence of different code pairs in the gene sequence have certain rules? Are these regularities related to translation rates in different regions of the gene? Is this relationship an important factor affecting the preference of passwords for use? These issues are extremely challenging topics in bioinformatics and genomics research, and the related research on the bovine genome is still blank

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 for detecting codon pair bias of bovine whole-genome
  • Method for detecting codon pair bias of bovine whole-genome
  • Method for detecting codon pair bias of bovine whole-genome

Examples

Experimental program
Comparison scheme
Effect test

Embodiment Construction

[0015] The present invention first obtains the bovine whole genome sequence from NCBI, and extracts all known protein coding sequences from the sequence. According to these protein coding sequences, the use preference scores of 3721 codon pairs were calculated, and then the codon pair use preference of the CDS sequence of each coding sequence was calculated. Finally, according to the codon pair usage distribution of each CDS sequence, the codon pair usage preference distribution of the whole genome was obtained by using the alignment analysis technique.

[0016] The present invention will be further described in detail below, which is an explanation of the present invention rather than a limitation.

[0017] a. Extraction of protein coding sequence of whole bovine genome

[0018] 1. Use UCSC's Table Browser to obtain the whole genome sequence and genome annotation information of cattle (TaxID: 9913).

[0019] 2. Use the self-compiled Java program to obtain all known bovine p...

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 for detecting codon pair bias of a bovine whole-genome. The method comprises the steps of: calculating codon pair score CPS of 3721 kinds of codon pairs in a CDS (coding sequence)of the bovine whole-genome; analyzing codon pair bias CPB of a single sequence in the bovine whole-genome according to the CPS of different codon pairs, wherein a CPB value of a sequence is an arithmetic average value of values of all codon pairs in the sequence; establishing a codon pair bias profile for each CDS in the genome according to the CPS of 3721 kinds of codon pairs in the genome and an arranging sequence of the codon pairs in the CDS ; aligning codon pair bias profiles of all CDS in the bovine genome form a 5' end and a 3' end of the sequence, and calculating an average value of the CPS of each codon pair locus in alignment results, thereby obtaining a whole-genome averaged codon pair bias profile of all CDS of the bovine.

Description

technical field [0001] The invention belongs to the field of molecular genetics and bioinformatics, relates to the detection of genome-specific biological information, in particular to a method for detecting the use preference of cattle whole-genome codes. Background technique [0002] According to the central dogma, the transmission of genetic information is from DNA to mRNA, and then from mRNA to protein. Genetic information is transmitted in the form of triplet codes during the transfer process from mRNA to protein. Each amino acid corresponds to at least one codon, and there are at most 6 corresponding codons. Codons that code for the same amino acid are called synonymous codons. People have conducted some studies on the codon usage bias of different species, and found that there are obvious biases in the usage of codons in different species; the codon usage bias of different functional genes in the same species is also quite different. There are 3721 (61×61) differen...

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
Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18
Inventor 刘小林张慧林赵胜
Owner NORTHWEST A & F UNIV
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Patsnap Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Patsnap Eureka Blog
Learn More
PatSnap group products

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

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap|About US| Contact US: help@patsnap.com