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Method and system for deducing bonding site of oligonucleotide on genome

A technology of oligonucleotides and binding sites, applied in the field of inferring oligonucleotide binding sites, which can solve problems such as low efficiency, complex calculations, and slow search processes

Inactive Publication Date: 2016-05-18
INST OF RADIATION MEDICINE ACAD OF MILITARY MEDICAL SCI OF THE PLA +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, for the calculation of the thermodynamic stability of hybridization between the designed oligonucleotide sequence and its binding sequence, in the prior art, this method is usually applied to the calculation of bases from front to back, that is, the idea of ​​traversal, the calculation is complicated, and the search process is slow. and less efficient

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  • Method and system for deducing bonding site of oligonucleotide on genome
  • Method and system for deducing bonding site of oligonucleotide on genome
  • Method and system for deducing bonding site of oligonucleotide on genome

Examples

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Embodiment 1

[0088] Example 1: Using figure 1 The determinative binding sequence module 12 in the system 10 for estimating oligonucleotide binding sites at the genome level as shown obtains the binding sequence of the oligonucleotide sequence to be deduced according to the method of the present invention

[0089] Step 1: use the index table construction module 11 in the system 10 to construct an index table of the thermodynamic information of any 7-mer oligonucleotide, the thermodynamic information is the pairwise hybridization of the oligonucleotide and all its binding sequences Information, including hybrid structure, hybrid sequence, enthalpy, entropy, and free energy;

[0090] 1) Each base (such as A) on any oligonucleotide will encounter five situations (T, A, G, C, -) in the binding sequence, so that 0, 1 in the pentadic number , 2, and 3 respectively correspond to one of the four kinds of deoxyribonucleic acid, and 4 corresponds to the gap. Any 7-mer oligonucleotide and all its bin...

Embodiment 2

[0131] Example 2 Use the positioning module 13 in the application system 10 to locate the position of the thermodynamically stable binding sequence obtained in Example 1 on the whole human genome

[0132] The known k-mer algorithm processing process is as follows:

[0133] (1) Using the sliding window method, set the window size to k-mer, and determine a total of 4 segments to be searched k sequence, where k=9,

[0134] (2) With a step size of 1, scan the 9-mer fragment to be searched from front to back on the specified genome,

[0135] (3) Record the positions of the 9-mer fragments to be searched on the positive and negative strands of different genes,

[0136] (4) Repeat (2) (3) process for all segments to be searched,

[0137] (5) Express the arbitrary 9-mer fragments appearing in the genome in the form of decimal numbers, and store the position information of each arbitrary 9-mer fragment on the genome together in the database.

[0138] The k-mer preprocessing algorit...

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Abstract

The invention provides a method and system for deducing a bonding site of oligonucleotide on a genome. According to the method, an index table of thermodynamics of arbitrary 7-mer oligonucleotide is built, a stable bonding sequence of the oligonucleotide to be deduced on the thermodynamics is acquired by using the index table, the position of the bonding sequence is positioned on the genome, thus, the bonding site of the oligonucleotide to be deduced can be efficiently deduced, and a basis is further provided for judging whether the oligonucleotide is high-quality oligonucleotide with regard to a target sequence in the genome. The invention also provides a system for the bonding site of the oligonucleotide on the genome. With the adoption of the above method by the system, the real bonding condition of the oligonucleotide and the target sequence in the genome can be efficiently reflected from the thermodynamics property, and an accurate basis can be provided for judging the quality of the oligonucleotide to be deduced.

Description

technical field [0001] The present invention relates to a method and system for estimating oligonucleotide binding sites, in particular to a method and system for estimating oligonucleotide binding sites on genome. Background technique [0002] Oligonucleotide (oligonucleotide or oligo) is a general term for a class of short-chain nucleotides. By matching with its complementary sequence, it is often used as a probe to determine the structure of the target gene, or as a primer to effectively amplify the template sequence. At present, molecular biotechnology based on oligonucleotide hybridization (such as chip probes, PCR primers, etc.) is widely used and plays an important role in the fields of next-generation sequencing, pathogenic microorganism detection, chip hybridization, and clinical diagnosis. The fundamental principle is nucleic acid molecular hybridization, that is, complementary nucleotide sequences form non-covalent bonds through Watson-Crick base pairing under cer...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18G06F17/30
Inventor 张成岗屈武斌刘哲言
Owner INST OF RADIATION MEDICINE ACAD OF MILITARY MEDICAL SCI OF THE PLA
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