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UTR query method and device based on Spark SQL

A query method and query statement technology, applied in the field of SparkSQL-based UTR query method and device, capable of solving problems such as limited algorithm efficiency and low UTRdb query efficiency

Inactive Publication Date: 2021-06-04
XIAN UNIV OF POSTS & TELECOMM
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the existing genetic data analysis based on RefGene, ResSeq and other databases is limited by the algorithm efficiency of the interval query of these two databases, resulting in very low query efficiency of UTRdb

Method used

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  • UTR query method and device based on Spark SQL
  • UTR query method and device based on Spark SQL

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Embodiment Construction

[0011] In order to make the object, technical solution and advantages of the present invention clearer, the present invention will be described in further detail below in conjunction with specific embodiments and with reference to the accompanying drawings.

[0012] refer to figure 1 , is a flowchart of an embodiment of the present invention.

[0013] The gene analysis annotation method comprises the following steps:

[0014] Step 101, use the specified Spark SQL statement to query the RefGene database, and return the ID that uniquely identifies the gene. The specified Spark SQL statement refers to the query statement select*from s rgjoin r on governlap((s.txStart,s.txEnd,s.exonCount,s.exonStarts,s.exonEnds,s.chr,s.strand), (r.start,r.end,r.chr)). In this query statement, s represents the RefGene database in table form, and r represents the variation to be annotated in table form. Use the two-tuple as the condition of on, and each parameter in the two-tuple is expressed as...

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Abstract

The embodiment of the invention provides a query method of UTR based on Spark SQL. The method comprises: querying a RefGene database by using a specified Spark SQL statement, and returning an ID of a unique identification gene; and querying the UTRdb according to the returned gene ID, and returning a query result. In addition, the embodiment of the invention provides a query device of the UTR based on the Spark SQL.

Description

technical field [0001] The invention relates to the technical field of gene detection, in particular to a Spark SQL-based UTR query method and device. Background technique [0002] Gene sequencing refers to the analysis of blood, body fluids or cells by sequencing instruments to measure the base sequence that makes up deoxyribonucleic acid (DNA). The 5' and 3' UTRs (untranslated regions) of eukaryotic mRNAs play critical roles in the post-transcriptional regulation of gene expression by regulating the transport, translation efficiency, subcellular localization, and message stability of nucleoplasmic mRNAs. UTRdb is a curated database of 5' and 3' eukaryotic mRNA untranslated sequences derived from multiple primary data sources. [0003] With the rapid decline in costs, gene sequencing is gradually moving towards clinical applications, and the sequencing data has shown explosive growth, and the data that needs to be analyzed for mutations has also increased dramatically. Ho...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F16/242G06F16/2455G16B40/00G16B50/00
CPCG06F16/2433G06F16/24553G16B40/00G16B50/00
Inventor 吕宁
Owner XIAN UNIV OF POSTS & TELECOMM