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Metadex : = The Metagenomic Data Exp...

ProQuest Information and Learning Co.

Metadex : = The Metagenomic Data Explorer.

紀錄類型:	書目-語言資料,手稿 : Monograph/item
正題名/作者:	Metadex :/
其他題名:	The Metagenomic Data Explorer.
作者:	Chandrashekhar, Vibhu.
面頁冊數:	1 online resource (31 pages)
附註:	Source: Masters Abstracts International, Volume: 57-04.
Contained By:	Masters Abstracts International57-04(E).
標題:	Information science. -
電子資源:	click for full text (PQDT)
ISBN:	9780355651553

Metadex : = The Metagenomic Data Explorer.
Chandrashekhar, Vibhu.

Metadex :The Metagenomic Data Explorer. - 1 online resource (31 pages)

Source: Masters Abstracts International, Volume: 57-04.

Thesis (M.S.)--San Diego State University, 2018.

Includes bibliographical references

The development of culture-independent methods has borne fruit; metagenomics and related fields are thriving thanks to the well-developed pipelines and decades of work. Given the increased proliferation of whole genome sequenced data, we can characterise metagenomic environments by function and taxonomy. Comparative metagenomics is based on determining features of interest from differentially abundant counts. Differential abundance does not imply importance to one's study, and can be the result of differences in diversity. A key question of interest in comparative metagenomics is to identify the role of environment on the functionome. Essentially, which gene functions are undergoing selection pressures in a given environment?

Electronic reproduction.
Ann Arbor, Mich. :
ProQuest,
2018

Mode of access: World Wide Web

ISBN: 9780355651553Subjects--Topical Terms:

561178
Information science.
Index Terms--Genre/Form:

554714
Electronic books.

Metadex : = The Metagenomic Data Explorer.
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264 0 $c 2018
300 $a 1 online resource (31 pages)
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500 $a Source: Masters Abstracts International, Volume: 57-04.
500 $a Adviser: Scott Kelley.
502 $a Thesis (M.S.)--San Diego State University, 2018.
504 $a Includes bibliographical references
520 $a The development of culture-independent methods has borne fruit; metagenomics and related fields are thriving thanks to the well-developed pipelines and decades of work. Given the increased proliferation of whole genome sequenced data, we can characterise metagenomic environments by function and taxonomy. Comparative metagenomics is based on determining features of interest from differentially abundant counts. Differential abundance does not imply importance to one's study, and can be the result of differences in diversity. A key question of interest in comparative metagenomics is to identify the role of environment on the functionome. Essentially, which gene functions are undergoing selection pressures in a given environment?
520 $a We present MetaDEx, a simple Python package for determining environmentally relevant functions and subsystems for comparative metagenomic data. The package receives annotations from MG-RAST and continues with a simple workflow for determining genes and subsystems of interest. To validate our tool, we ran MetaDEx with MG-RAST data for two Moroccan lagoons: Nador and Oualidia. Here we show how it was used to determine environmentally relevant functional categories, including genes for photosynthesis and bilin biosynthesis.
520 $a MetaDEx combines a variety of data-wrangling methods in a simple and sequential workflow, simplifying the comparative metagenomic goal of determining important features. It is available under MIT license through PyPI.
533 $a Electronic reproduction. $b Ann Arbor, Mich. : $c ProQuest, $d 2018
538 $a Mode of access: World Wide Web
650 4 $a Information science. $3 561178
650 4 $a Biology. $3 599573
650 4 $a Medicine. $3 644133
655 7 $a Electronic books. $2 local $3 554714
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690 $a 0306
690 $a 0564
710 2 $a ProQuest Information and Learning Co. $3 1178819
710 2 $a San Diego State University. $b Bioinformatics and Medical Informatics. $3 1195568
773 0 $t Masters Abstracts International $g 57-04(E).
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10745834 $z click for full text (PQDT)

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