MultiGeneBlast statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MultiGeneBlast
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Tool usage distribution map

This map represents all the scientific publications referring to MultiGeneBlast per scientific context
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Protocols

MultiGeneBlast specifications

Information


Unique identifier OMICS_14735
Name MultiGeneBlast
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data An annotated genome sequence
Input format GBK, EMBL
Output data An interactive XHTML page, in which additional information on each gene appears on mouse-over or by clicking on a gene.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Medium
Version 1.1.13
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Eriko Takano

Publication for MultiGeneBlast

MultiGeneBlast citations

 (25)
library_books

Biosynthetic pathway for furanosteroid demethoxyviridin and identification of an unusual pregnane side chain cleavage

2018
Nat Commun
PMCID: 5943271
PMID: 29743477
DOI: 10.1038/s41467-018-04298-2

[…] -chain cleavage mediated by VidF, VidP, and VidH is the predominant mechanism in fungal steroid biosynthesis (Fig. ). Consistent with this speculation, a homology search of VidF, VidP, and VidH using MultiGeneBlast at the NCBI database revealed that these gene clusters are widely distributed in fungal genomes, suggesting that the three-enzyme-mediated pregnane side-chain cleavage is likely to be a […]

library_books

Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes

2018
Appl Environ Microbiol
PMCID: 5930311
PMID: 29500259
DOI: 10.1128/AEM.02828-17

[…] RefSeq nucleotide database (i.e., genomic sequences containing the protein identifications [IDs] recovered from BLASTP). This yielded a total of 754 nucleotide records which were then analyzed using MultiGeneBlast () to ascertain which ones had the complete bcm gene cluster. Thirty of the 754 sequences were discarded on the basis that they did not contain the bcm gene cluster or that the sequence […]

library_books

Biosynthesis of fragin is controlled by a novel quorum sensing signal

2018
Nat Commun
PMCID: 5878181
PMID: 29602945
DOI: 10.1038/s41467-018-03690-2

[…] Protein domains were analyzed with the NRPS/PKS analysis tool, NaPDoS (Natural Product Domain Seeker) and the InterProSCan 5 online tool.The architecture search mode of the MultiGeneBlast software was used to identify gene clusters similar to the ham cluster in other bacteria. The amino acid sequences of all Ham proteins (HamA–HamG) were combined in one fasta file and us […]

library_books

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

2018
Genome Biol Evol
PMCID: 5765558
PMID: 29319806
DOI: 10.1093/gbe/evx271

[…] sing an e-value of 1.0E−7 as cut-off. The presence of Type III secretion systems (T3SSs), Type IV secretion systems (T4SSs), and Type VI secretion systems (T6SSs) was investigated in the genomes with MultiGeneBlast 1.1.14 () using default settings with as query previously identified gene clusters that were described by , that is, FO-BEG1_3657-03696 (T3SS), PsW64_00918-00938 (T4SS), FO-BEG1_01844-0 […]

library_books

Large Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology

2017
mSystems
PMCID: 5686519
PMID: 29152584
DOI: 10.1128/mSystems.00040-17

[…] he R fpc library was used in conjunction with the previously produced submatrices to cluster BGCs. DBSCAN uses two key parameters for its algorithm: EPS and min pts. DBSCAN clusters the BGCs by their MultiGeneBlast scores if a certain number of BGCs (min pts) fall within a certain radius (EPS). DBSCAN parameters were optimized by iteratively running DBSCAN and varying the EPS by 0.01 (from 0.01 to […]

call_split

A phylogenetic and evolutionary analysis of antimycin biosynthesis

2017
Microbiology
PMCID: 5883857
PMID: 29111964
DOI: 10.1099/mic.0.000572
call_split See protocol

[…] Prokka 1.12 []. Next, annotated GenBank files were modified using the Unix commands grep and sed to move the unique gene prefix generated by Prokka from the ‘/locus_tag’ field to the ‘/gene’ field. A multigeneblast database was created using the makedb programme of multigeneblast version 1.1.13 and the processed GenBank files from above []. The genes antFGHIJKLMNOPQ of the antimycin BGC from S. am […]


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MultiGeneBlast institution(s)
Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands; Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands; Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK; Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
MultiGeneBlast funding source(s)
This work was supported by the Dutch Technology Foundation STW, which is the applied science division of NWO, the Technology Programme of the Ministry of Economic Affairs (grant number STW 10463), an NWO-Vidi fellowship, and a Rosalind Franklin Fellowship, University of Groningen.

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