MultiGeneBlast protocols

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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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  • person_outline Eriko Takano <>

Publication for MultiGeneBlast

MultiGeneBlast in pipelines

 (2)
2017
PMCID: 5488378
PMID: 28655355
DOI: 10.1186/s12864-017-3886-0

[…] then manually corrected through the rast server using seed annotation tools []. prophage-like sequences at the gene cluster level in ncbi genbank bacterial genomes (01/2015) were detected by using a multigeneblast (v1.1.14) architecture search with vb_thps-p1, vb_peas-p1, and vb_cibm-p1 genomes as queries []. the prophage identification tool phage search tool (phast) was used to determine […]

2017
PMCID: 5489566
PMID: 28706512
DOI: 10.3389/fmicb.2017.01204

[…] 3 and antismash 3.0, respectively (zhou et al., ; dhillon et al., ; weber et al., ). the whole genome sequences were submitted to the different tools, and the identified clusters compared using multigeneblast (medema et al., )., genome sequences were analyzed in crisprfinder (grissa et al., ) and homology searches for crispr associated genes were performed using clc main workbench. using […]


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MultiGeneBlast in publications

 (22)
PMCID: 5943271
PMID: 29743477
DOI: 10.1038/s41467-018-04298-2

[…] 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 […]

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 […]

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

[…] in the ham cluster, hamg, encodes an aminotransferase that most likely adds an amino group to the biosynthetic product of the ham cluster (fig. ). an architecture search of the ham cluster with the multigeneblast software showed that homologs of the ham cluster are present in several b. cenocepacia strains and in burkholderia cepacia dds 7h-2 (supplementary data ). the hamabcde operon is also […]

PMCID: 5765558
PMID: 29319806
DOI: 10.1093/gbe/evx271

[…] 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), […]

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

[…] representatives of 23 characterized bacillus bgcs (where a natural product is associated with a bgc [see in the supplemental material]) were combined with these predicted bgcs for a 19,985-member multigeneblast (mgb) library. the bgcs were analyzed using multigeneblast (), a program that does an all-by-all comparison and calculates an mgb score for each bgc pair based on the synteny […]


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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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