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Method and system for identification and classification of operational taxonomic units in a metagenomic sample

A technology for manipulating taxa and metagenomics, applied in the field of manipulating taxa, can solve suboptimal and inaccurate problems

Active Publication Date: 2019-07-16
TATA CONSULTANCY SERVICES LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Since the query reads / sequences used during comparison are only "short reads", the results of OTU identification / classification may be inaccurate and sub-optimal

Method used

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  • Method and system for identification and classification of operational taxonomic units in a metagenomic sample
  • Method and system for identification and classification of operational taxonomic units in a metagenomic sample
  • Method and system for identification and classification of operational taxonomic units in a metagenomic sample

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Embodiment Construction

[0018] Embodiments herein and their various features and advantageous details are explained more fully with reference to the non-limiting embodiments shown in the drawings and detailed in the following description. The examples used herein are intended merely to facilitate an understanding of ways in which the embodiments herein may be practiced and to enable further practice of the embodiments herein by those skilled in the art. Accordingly, these examples should not be construed as limiting the scope of the embodiments described herein.

[0019] Vocabulary used in the implementation - Terminology

[0020] In the context of the present disclosure, the expression "operational taxonomic unit" or "OTU" refers to sequences that have been clustered together (with significant sequence similarity) and can be considered to be derived from the same group of organisms. Typically, operational taxonomies are defined based on similarity thresholds. Although the customized OTU database i...

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Abstract

A system and method for identification and classification of operational taxonomic units (OTUs) in a metagenomic sample using short read amplicon sequences has been described. The disclosure enables accurate identification of OTU in a metagenomic sample and provides a framework for easy cross comparison of microbiome community structures sampled across different disconnected metagenomic studies. Instead of using a reference database consisting of full-length marker genes directly for taxonomic classification or OTU-picking, the present disclosure creates customized OTU databases for differenthyper-variable regions of a marker gene. These databases consist of reference OTUs obtained through independent clustering of sequences pertaining to different selected hyper-variable regions of the marker gene. In another embodiment, mapping back is also provided facilitating cross comparison between results obtained from different studies that may have utilized different hyper-variable regions.The system results in enhanced accuracy of classification of operational taxonomic units (OTUs) in the metagenomic sample.

Description

[0001] Cross References and Priority to Related Applications [0002] This application claims priority to Indian non-provisional specification no. 201721027000 filed on 28 July 2017, the entire disclosure of which is hereby incorporated by reference in its entirety. technical field [0003] Embodiments herein relate generally to the field of improving the accuracy of taxonomic classification of metagenomic samples, and more specifically, to methods and methods for using short-read amplicon sequences to identify and classify operational taxa in metagenomic samples. system. Background technique [0004] Metagenomic studies use DNA sequencing of phylogenetic marker genes to determine microbial community structure in relation to sampled environments and taxonomic classifications for inhabiting microbial organisms. However, the current generation of cost-effective high-throughput DNA sequencing technologies can only generate short 'shot 'reads' (fragments of DNA sequence approxi...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/00G16B30/10G16B50/30G16B50/10G16B30/00G16B40/00
CPCG16B30/00G16B40/00G16B50/10C12Q1/689C12Q2600/158G16B40/10G16B10/00G16B20/00G16B50/00C12Q1/6809C12Q1/6869
Inventor S·S·曼德D·亚达夫A·杜塔
Owner TATA CONSULTANCY SERVICES LTD