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TGTP-DB – a database for extracting genome, transcriptome and proteome data using taxonomy (CROSBI ID 639105)

Prilog sa skupa u zborniku | izvorni znanstveni rad | međunarodna recenzija

Križanović, Krešimir ; Marinović, Mladen ; Bulović, Ana ; Vaser, Robert ; Šikić, Mile TGTP-DB – a database for extracting genome, transcriptome and proteome data using taxonomy // Proceedings of the 39th International Convention Mipro 2016, Distributed Computing, Visualization and Biomedical Engineering /DC VIS / Biljanović, Petar (ur.). Rijeka: Hrvatska udruga za informacijsku i komunikacijsku tehnologiju, elektroniku i mikroelektroniku - MIPRO, 2016. str. 472-476

Podaci o odgovornosti

Križanović, Krešimir ; Marinović, Mladen ; Bulović, Ana ; Vaser, Robert ; Šikić, Mile

engleski

TGTP-DB – a database for extracting genome, transcriptome and proteome data using taxonomy

An enormous potential of metagenomics has caused a significantly increased research activity in recent years. However, discovering pathogens present in a metagenomics sample is still inadequately accurate and very time consuming. Narrowing down a list of potential pathogens would significantly decrease the referent database size and thus improve both accuracy and speed. While publicly available databases enable free access to all their data, the interface is generally unwieldy and impractical for producing concrete reference datasets quickly, making the process either very time consuming or requiring significant programming skills. Relatively simple and sufficiently powerful tools allowing the users to quickly extract desired reference datasets would make metagenomic tools readily available to a larger number of researchers. In this paper we present a set of scripts for downloading publicly available data on taxonomy, genomes, transcriptomes and proteomes and loading it into a relational database. This enables the user to use SQL and other standard relational database tools to search and extract specific datasets. The power and ease of use of the TGTP-DB is demonstrated with a search engine that allows the user to search the taxonomy tree for a desired group of organisms, and download files containing genomes, transcriptomes or proteomes of the organisms in the group.

trancriptome; genome; proteome; database; taxonomy

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Podaci o prilogu

472-476.

2016.

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objavljeno

978-953-233-087-8

Podaci o matičnoj publikaciji

Proceedings of the 39th International Convention Mipro 2016, Distributed Computing, Visualization and Biomedical Engineering /DC VIS

Biljanović, Petar

Rijeka: Hrvatska udruga za informacijsku i komunikacijsku tehnologiju, elektroniku i mikroelektroniku - MIPRO

Podaci o skupu

MIPRO 2016

predavanje

30.05.2016-03.06.2016

Opatija, Hrvatska

Povezanost rada

Računarstvo