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

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

Vrsta, podvrsta i kategorija rada
Radovi u zbornicima skupova, cjeloviti rad (in extenso), znanstveni

Izvornik
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, 2016, 472-476

ISBN
978-953-233-087-8

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

Mjesto i datum
Opatija, Hrvatska, 30.05.2016. - 03.06.2016

Vrsta sudjelovanja
Predavanje

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
trancriptome; genome; proteome; database; taxonomy

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Računarstvo

POVEZANOST RADA