PMID- 23065606
OWN - NLM
STAT- MEDLINE
DCOM- 20130311
LR  - 20220311
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 944
DP  - 2012
TI  - Bioinformatics approaches and software for detection of secondary metabolic gene 
      clusters.
PG  - 23-45
LID - 10.1007/978-1-62703-122-6_2 [doi]
AB  - The accelerating pace of microbial genomics is sparking a renaissance in the 
      field of natural products research. Researchers can now get a preview of the 
      organism's secondary metabolome by analyzing its genomic sequence. Combined with 
      other -omics data, this approach may provide a cost-effective alternative to 
      industrial high-throughput screening in drug discovery. In the last few years, 
      several computational tools have been developed to facilitate this process by 
      identifying genes involved in secondary metabolite biosynthesis in bacterial and 
      fungal genomes. Here, we review seven software programs that are available for 
      this purpose, with an emphasis on antibiotics & Secondary Metabolite Analysis 
      SHell (antiSMASH) and Secondary Metabolite Unknown Regions Finder (SMURF), the 
      only tools that can comprehensively detect complete secondary metabolite 
      biosynthesis gene clusters. We also discuss five related software 
      packages-CLUster SEquence ANalyzer (CLUSEAN), ClustScan, Structure Based Sequence 
      Analysis of Polyketide Synthases (SBSPKS), NRPSPredictor, and Natural Product 
      searcher (NP.searcher)-that identify secondary metabolite backbone biosynthesis 
      genes. This chapter offers detailed protocols, suggestions, and caveats to assist 
      researchers in using these tools most effectively.
FAU - Fedorova, Natalie D
AU  - Fedorova ND
AD  - The J. Craig Venter Institute, Rockville, MD, USA. natalief@jcvi.org
FAU - Moktali, Venkatesh
AU  - Moktali V
FAU - Medema, Marnix H
AU  - Medema MH
LA  - eng
GR  - HHSN272200900007C/PHS HHS/United States
GR  - N01-AI-30071/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (Anti-Bacterial Agents)
RN  - 0 (Biological Products)
RN  - 79956-01-7 (Polyketide Synthases)
SB  - IM
MH  - Algorithms
MH  - Anti-Bacterial Agents/pharmacology
MH  - Bacteria/drug effects/*genetics/*metabolism
MH  - Biological Products/metabolism
MH  - Computational Biology/*methods
MH  - Fungi/drug effects/*genetics/*metabolism
MH  - Genomics
MH  - Internet
MH  - Multigene Family/*genetics
MH  - Polyketide Synthases/genetics
MH  - *Software
EDAT- 2012/10/16 06:00
MHDA- 2013/03/12 06:00
CRDT- 2012/10/16 06:00
PHST- 2012/10/16 06:00 [entrez]
PHST- 2012/10/16 06:00 [pubmed]
PHST- 2013/03/12 06:00 [medline]
AID - 10.1007/978-1-62703-122-6_2 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2012;944:23-45. doi: 10.1007/978-1-62703-122-6_2.