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Microbial genome browsing


Hranueli, Daslav; Starcevic, Antonio; Zucko, Jurica; Diminić, Janko; Gacesa, Ranko; Branasic, Damir; Long, F Paul; Cullum, John
Microbial genome browsing // Book of Abstracts / Silvija Černi, Martina Šeruga Musić, Dijana Škorić (ur.).
Zagreb: Hrvatsko mikrobiološko društvo, 2012. str. 21-21 (pozvano predavanje, domaća recenzija, sažetak, znanstveni)


Naslov
Microbial genome browsing

Autori
Hranueli, Daslav ; Starcevic, Antonio ; Zucko, Jurica ; Diminić, Janko ; Gacesa, Ranko ; Branasic, Damir ; Long, F Paul ; Cullum, John

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
Book of Abstracts / Silvija Černi, Martina Šeruga Musić, Dijana Škorić - Zagreb : Hrvatsko mikrobiološko društvo, 2012, 21-21

Skup
5th Croatian Congres of Microbiology with International Participation

Mjesto i datum
Primošten, Hrvatska, 26-30.9.2012

Vrsta sudjelovanja
Pozvano predavanje

Vrsta recenzije
Domaća recenzija

Ključne riječi
DNA sequencing technology; 454 Genome Sequencer FLX instrument; metagenomes; bioinformatics expert system

Sažetak
The rapid progress in DNA sequencing technology is resulting in exponentially growing microbial genome sequences, but the increase in laboratory-derived information on protein function is much slower. In many cases, standard bioinformatics methods can assign genes to a family, but the exact function of the encoded protein remains unknown. Moreover, the generation of high quality DNA sequence is disproportionately time consuming and expensive. The dramatic fall in sequencing costs means that genome sequencing is tending to become an experimental technique, which is used as part of the strategy for tackling a research problem, rather than an aim in itself. It is, therefore, important to develop methods for the structural and functional automatic annotation for the analysis of lower quality sequence starting from DNA reads generated, for example, by the 454 Genome Sequencer FLX instrument. We have developed the bioinformatics expert system for the structural and functional automatic annotation of microbial genomes and metagenomes that allows simple browsing of DNA reads. The expert system consists of structural and functional annotation that runs on a server as a bioinformatics "black box" and the Web based graphical user interface for sequence interrogation. Unlike most other systems, the initial functional analysis is carried out on reads before assembly. The reads are translated in silico and the resulting protein sequences scanned using HMM-profiles. Depending on the aims of the analysis, it is possible to use a generic library of profiles (e.g. corresponding to the classification in the KEGG database) or a custom databases of choice (e.g. to detect particular classes of enzymes in metagenomic data). The reads are subsequently assembled (e.g. using the Newbler whole-genome sequence assembler). The assembled sequences can be used for "gene of interest" (GOl) analysis by BLAST and/or InterproScan that are also integrated within the expert system. The user can browse the sequences for GOls with the Solr search engine, which is implemented within the graphical user interface. An example of a recently sequenced microbial genome will be used to demonstrate the functionality of the expert system. The aim is to provide a flexible intuitive system for browsing microbial genomic sequences and metagenomic sequences, which allows the user to "Google" the data.

Izvorni jezik
Engleski

Znanstvena područja
Biotehnologija



POVEZANOST RADA


Projekt / tema
058-0000000-3475 - Generiranje potencijalnih lijekova u uvjetima in silico (Daslav Hranueli, )

Ustanove
Prehrambeno-biotehnološki fakultet, Zagreb