NDLI: antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Content Provider	PubMed Central
Author	Weber, Tilmann Blin, Kai Srikanth, Duddela Krug, Daniel Kim, Hyun Uk Bruccoleri, Robert Lee, Sang Yup Fischbach, Michael A. Müller, Rolf Wohlleben, Wolfgang Breitling, Rainer Takano, Eriko Medema, Marnix H.
Copyright Year	2015
Abstract	Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.
Related Links	http://dx.doi.org/10.1093/nar/gkv437
Starting Page	237
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	Web Server issue
Volume Number	43
Language	English
Publisher	Oxford University Press
Publisher Date	2015-07-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters

The Integration of Genome Mining, Comparative Genomics, and Functional Genetics for Biosynthetic Gene Cluster Identification

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters

Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

Mining biosynthetic gene clusters in Virgibacillus genomes

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Similar Documents

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters

The Integration of Genome Mining, Comparative Genomics, and Functional Genetics for Biosynthetic Gene Cluster Identification

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters

Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

Mining biosynthetic gene clusters in Virgibacillus genomes

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters