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Informatics-based gene transcript assembly and quantification method and system

A technology for gene transcripts and quantification methods, applied in the field of gene transcript assembly and quantification methods and systems based on information theory, can solve problems such as limited accuracy, and achieve the effects of improving accuracy, improving sequencing accuracy, and improving gene assembly accuracy

Active Publication Date: 2018-04-20
TSINGHUA UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, the accuracy of the methods in the current related technologies is limited and needs to be further improved.
And although the mathematical underpinnings of these methods are very similar, there are large differences in the transcripts discovered by these different methods

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  • Informatics-based gene transcript assembly and quantification method and system
  • Informatics-based gene transcript assembly and quantification method and system
  • Informatics-based gene transcript assembly and quantification method and system

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Embodiment Construction

[0025] Embodiments of the present invention are described in detail below, examples of which are shown in the drawings, wherein the same or similar reference numerals designate the same or similar elements or elements having the same or similar functions throughout. The embodiments described below by referring to the figures are exemplary and are intended to explain the present invention and should not be construed as limiting the present invention.

[0026] figure 1 It is a flowchart of a method for assembling and quantifying gene transcripts based on information theory according to an embodiment of the present invention and figure 2 A flow chart of the technical implementation of the gene transcript assembly and quantification method based on information theory according to an embodiment of the present invention. combine figure 1 and figure 2 , the method includes the following steps:

[0027] S1, align the sequenced reads with the reference genome, and predict the sta...

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Abstract

The invention provides an informatics-based gene transcript assembly and quantification method and system, wherein the method comprises: aligning a sequencing read with a reference genome, and predicting initial start and end positions of a gene and transcript according to the alignment results for the sequencing read and reference genome; after prediction, establishing a directed graph to simulate possible transcripts to obtain a candidate transcript set; subjecting the candidate transcript set to transcript prediction and kurtosis estimation according the mode of maxium information transmission capacity. The method and system of the invention have the advantages that dependence on external gene positional marking is avoided, gene assembly accuracy is significantly improved, and sequencing precision is improved.

Description

technical field [0001] The invention relates to the technical field of computational biology, in particular to a method and system for assembling and quantifying gene transcripts based on information theory. Background technique [0002] With the development of next-generation gene sequencing technology, gene biology research urgently needs effective quantitative methods to analyze the internal gene regulation and transcription of high-throughput RNA sequencing. At the RNA level, the identification and abundance estimation of transcripts is an important method to evaluate the differences in transcriptional functions. In next-generation sequencing research, it can reveal the underlying mechanism of diseases and discover new biological conclusions. Transcript assembly is the expression of transcript variants from structured restorer genes in large-scale sequencing reads. Kurtosis estimation is a quantitative estimate of the expression levels of discovered transcripts. Howeve...

Claims

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Application Information

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IPC IPC(8): G06F19/20
CPCG16B25/00
Inventor 索津莉鲍峰戴琼海
Owner TSINGHUA UNIV
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