Napredna pretraga

Pregled bibliografske jedinice broj: 448506

ClustScan : an integrated program package for the detection and semi-automatic annotation of secondary metabolite clusters in genomic and metagenomic DNA data sets


Cullum, John; Starčević, Antonio; Žučko, Jurica; Diminić, Janko; Long, Paul F.; Hranueli, Daslav
ClustScan : an integrated program package for the detection and semi-automatic annotation of secondary metabolite clusters in genomic and metagenomic DNA data sets // Handbook of Molecular Microbial Ecology, Volume I: Metagenomics and Complementary Approaches / de Bruijn, J. Frans (ur.).
Hoboken: John Wiley & Sons, Inc., 2011. str. 423-432


Naslov
ClustScan : an integrated program package for the detection and semi-automatic annotation of secondary metabolite clusters in genomic and metagenomic DNA data sets

Autori
Cullum, John ; Starčević, Antonio ; Žučko, Jurica ; Diminić, Janko ; Long, Paul F. ; Hranueli, Daslav

Vrsta, podvrsta i kategorija rada
Poglavlja u knjigama, znanstveni

Knjiga
Handbook of Molecular Microbial Ecology, Volume I: Metagenomics and Complementary Approaches

Urednik/ci
De Bruijn, J. Frans

Izdavač
John Wiley & Sons, Inc.

Grad
Hoboken

Godina
2011

Raspon stranica
423-432

ISBN
978-0-470-92418-1

Ključne riječi
Polyketides, non-ribosomal peptides, Actinomycetes, metagenomes, genomes, gene clusters, annotation, generic programme package

Sažetak
Clustscan ("Cluster Scanner") is a semi-automatic DNA sequence analysis tool. It has a server-client architecture, with analysis being carried out on the server and a Java user interface for the client, which can be a PC, Mac or Linux machine. Using collapsible tree overviews and zoom functions, it is possible to work with whole genomes or large sets of metagenomic data. Using custom profiles it is possible to quickly identify secondary metabolite clusters. For modular biosynthetic clusters (polyketide synthases and non-ribosomal peptide synthetases), the cluster hierarchical architecture is represented by the program and allows prediction of product chemistry that can be exported in a standard chemical format (SMILES). The user can examine the basis of predictions made and override them if necessary. An open architecture allows easy extension of the scope of the program. The program package allows rapid scanning of large DNA data sets to identify interesting clusters of genes. This chapter reviews the subsequent development of a system published in 2008 [Starcevic et al., 2008] for the semi-automatic annotation of modular biosynthetic gene clusters from different sources, including metagenomes from free-living and symbiotic microorganisms and, in silico prediction of novel chemical structures.

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