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Tytuł:
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Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects.
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Autorzy:
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Meunier L; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium.; Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro UMRT 1158, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium.
Tocquin P; InBioS-PhytoSYSTEMS, Plant Physiology, University of Liège, B-4000 Liège, Belgium.; Hedera-22 SCRL, B-4130 Tilff, Belgium.
Cornet L; GIGA institute, Medical Genomics-Unit of Animal Genomics, University of Liège, B-4000 Liège, Belgium.
Sirjacobs D; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium.
Leclère V; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, Joint Research Unit BioEcoAgro UMRT 1158, F-59000 Lille, France.
Pupin M; UMR 9189- CRIStAL- Centre de Recherche en Informatique Signal et Automatique de Lille, University of Lille, CNRS, Centrale Lille, F-59000 Lille, France.; Bonsai Team, Inria-Lille Nord Europe, F-59655 Villeneuve d'Ascq Cedex, France.
Jacques P; Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro UMRT 1158, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium.
Baurain D; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium.; Hedera-22 SCRL, B-4130 Tilff, Belgium.
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Źródło:
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Bioinformatics (Oxford, England) [Bioinformatics] 2020 Aug 01; Vol. 36 (15), pp. 4345-4347.
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Typ publikacji:
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Journal Article; Research Support, Non-U.S. Gov't
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Język:
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English
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Imprint Name(s):
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Original Publication: Oxford : Oxford University Press, c1998-
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MeSH Terms:
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Biosynthetic Pathways*
Software*
Bacteria/genetics ; Molecular Sequence Annotation ; Multigene Family
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Entry Date(s):
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Date Created: 20200517 Date Completed: 20210201 Latest Revision: 20210201
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Update Code:
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20240105
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DOI:
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10.1093/bioinformatics/btaa517
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PMID:
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32415965
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Summary: To support small and large-scale genome mining projects, we present Post-processing Analysis tooLbox for ANTIsmash Reports (Palantir), a dedicated software suite for handling and refining secondary metabolite biosynthetic gene cluster (BGC) data annotated with the popular antiSMASH pipeline. Palantir provides new functionalities building on NRPS/PKS predictions from antiSMASH, such as improved BGC annotation, module delineation and easy access to sub-sequences at different levels (cluster, gene, module and domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database.
Availability and Implementation: Palantir is released both as a Perl API available on CPAN (https://metacpan.org/release/Bio-Palantir) and as a web application (http://palantir.uliege.be). As a practical use case, the web interface also features a database built from the mining of 1616 cyanobacterial genomes, of which 1488 were predicted to encode at least one BGC.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
