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Database-driven primary analysis of raw sequencing data

A database and sequence technology, applied in the field of identifying possible sources of biological sequences, to achieve the effect of reducing time and computer processing power

Inactive Publication Date: 2015-09-16
DANMARKS TEKNISKE UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

The patent application does not disclose a method in which a set of runts in one reference sequence is searched for the presence of a runt and a set of positions in the reference sequence is searched for a position

Method used

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  • Database-driven primary analysis of raw sequencing data
  • Database-driven primary analysis of raw sequencing data
  • Database-driven primary analysis of raw sequencing data

Examples

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Embodiment 2

[0262] In this example, tens of thousands of genomes and genomic regions from bacteria, viruses, phages, plasmids, as well as humans, mice, plants, fungi, and archaea are referenced. A client running on a web browser was also implemented and demonstrated to process and identify gigabytes of raw sequencing data from a commercially available portable computing device in seconds while consuming a modest amount of bandwidth and Server communication. Thus, in this example, it is shown that identification of DNA from raw reads can be as simple as querying a search engine.

[0263] Query a DNA sequence against a comprehensive set of matches for a reference

[0264]The subjective way to find alignment programs is to divide them into two main categories: those that try to map a query sequence against a set of known references (such as BLAST), and those that try to map a large number of sequences against a given reference as quickly as possible. Short sequences (eg, Bowtie or BWA). ...

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Abstract

The present invention relates to methods for identifying the source of a biological sequence containing sample from raw sequencing reads. The method may be used to identify the source of unknown DNA and can be used for diagnostic, biodefense, food safety and quality, and hygiene applications. In another aspect the invention relates to a database of reference sequences which can be used in the method of the invention.

Description

field of invention [0001] The present invention relates to a method for identifying possible sources of biological sequences. In a further aspect, the invention relates to a database suitable for this purpose. Background of the invention [0002] DNA sequencing is the experimental process of identifying the sequence of bases (A, T, C, or G). As of today, no technology is capable of sequencing the complete molecule of DNA beyond a few kilobases, and most technologies sequence between 100 and 200 bases. Bacterial genomes can easily contain millions of bases. Over the past few years, the cost of sequencing has dropped dramatically, making it increasingly common to sequence DNA at scale in samples for purposes such as human health, food quality control, or microbial community research. It is conceivable that whole human genome sequencing will be used more frequently in therapy to personalize treatment as much as possible, and routine sequencing will be performed to control fo...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22G16B30/10G16B30/20G16B50/30
CPCG06F19/22G06F19/28G16B30/00G16B50/00G16B30/10G16B50/30G16B30/20
Inventor L·戈蒂埃O·伦德
Owner DANMARKS TEKNISKE UNIV
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