GenomeMatcher protocols

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GenomeMatcher specifications

Information


Unique identifier OMICS_00936
Name GenomeMatcher
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Two DNA sequences
Input format DDBJ/GenBank, single FASTA, plain text
Output data Graphical view of identity score of blastn comparison
Output format PDF, TIFF
Operating system Mac OS
Programming languages Objective-C
License Other
Computer skills Medium
Version 2.18
Stability Stable
Maintained Yes

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Publication for GenomeMatcher

GenomeMatcher in pipelines

 (8)
2017
PMCID: 5334596
PMID: 28254989
DOI: 10.1128/genomeA.01743-16

[…] the result was manually inspected with respect to positions of start codons for predicted open reading frames (orfs) using the microbial genome annotation pipeline (migap; http://www.migap.org/) and genomematcher ()., the genome of usda 122 consists of a single chromosome (9,136,536 bp, 64.0% g+c). a total of 8,551 protein-coding genes, 51 trnas, and three rrnas were predicted on the genome. […]

2017
PMCID: 5737509
PMID: 28338901
DOI: 10.1093/dnares/dsx011

[…] center for biotechnology information database (http://www.ncbi.nlm.nih.gov/ (1 march 2017, date last accessed)). the genome synteny plot of the chromosomes of the two strains was drawn using genomematcher. circular plots of the chromosomes and plasmids were drawn using arcwithcolor ver. 1.4, an accessory tool of genomematcher. protein alignments were analysed using clustal x. homology […]

2016
PMCID: 5017802
PMID: 27431195
DOI: 10.1264/jsme2.ME15159

[…] of strains doa1 and maff107635 containing runs of ns that represent gaps were used as inputs. all predicted gap lengths were less than 5 kb. organizations of nif–clusters were compared using genomematcher version 1.861 ()., the tested strains for phylogenetic and molecular evolutionary analyses are listed in . in addition to the newly genome-sequenced strains maff107635 and doa1, we used […]

2015
PMCID: 4676552
PMID: 26582551
DOI: 10.1264/jsme2.ME15080

[…] the genome sequences of bradyrhizobium sp. sutn9-2 (accession number laxe00000000) were compared with the whole genome of b. diazoefficiens usda110 () using the program genomematcher () at the amino acid level. the annotated genome sequences of usda110 (accession number ba000040) were obtained from genome assembly/annotation projects (ncbi database). the sequences […]

2013
PMCID: 3656210
PMID: 23682148
DOI: 10.1128/genomeA.00247-13

[…] we used genofinisher and acefileviewer (). annotation by the prokaryotic genome annotation pipeline (pgaap; http://www.ncbi.nlm.nih.gov/) was manually curated by using a dedicated tool bundled with genomematcher (), as well as by consulting the microbial genome annotation pipeline (migap) for auto annotation (http://www.migap.org/)., the mm-1 genome consists of one circular chromosome […]


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GenomeMatcher in publications

 (43)
PMCID: 5622343
PMID: 28957464
DOI: 10.1093/gbe/evx183

[…] as to whether they were located in the recombination tracts predicted by fastgear (see below). pairwise blastn analysis for chromosomal regions containing east asian alleles was performed using genomematcher software ()., population structure was inferred using baps6 software, assuming that mah is a recombinogenic bacterium. for this analysis, core genome snps were first detected by parsnp […]

PMCID: 5561799
PMID: 28861055
DOI: 10.3389/fmicb.2017.01540

[…] database (card) (mcarthur et al., ). insertion sequences (iss) were identified by an is finder (siguier et al., ). in addition, genomic sequences around the tetw gene were compared using a genomematcher to reveal the insertion of a putative tetw mobile cassette (ohtsubo et al., )., in addition to the seven strains (45, 53, 194, 195, 196, 197, and 198), three type strains, b. […]

PMCID: 5440377
PMID: 28533514
DOI: 10.1038/s41598-017-02381-0

[…] petrimonas and clostridium species were also present, corresponding to our 16s rrna gene analysis., the genome sequence was compared to the genome sequences of various dehalococcoides spp. using genomematcher (supplementary fig. ). the results clearly show that d. mccartyi uch-atv1 has high homology with d. mccartyi 195., the results of the gene annotation are summarized in table . compared […]

PMCID: 5334596
PMID: 28254989
DOI: 10.1128/genomeA.01743-16

[…] the result was manually inspected with respect to positions of start codons for predicted open reading frames (orfs) using the microbial genome annotation pipeline (migap; http://www.migap.org/) and genomematcher ()., the genome of usda 122 consists of a single chromosome (9,136,536 bp, 64.0% g+c). a total of 8,551 protein-coding genes, 51 trnas, and three rrnas were predicted on the genome. […]

PMCID: 5331512
PMID: 28183772
DOI: 10.1128/genomeA.01619-16

[…] (), and the result was manually inspected with respect to positions of start codons for predicted open reading frames using the microbial genome annotation pipeline (migap; http://www.migap.org) and genomematcher ()., the j5 genome consisted of a single chromosome (10,138,651bp, 63.3% g+c) and 9,067 coding sequences (cdss). the genome size and cds numbers were the highest among complete genomes […]


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GenomeMatcher institution(s)
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
GenomeMatcher funding source(s)
This work was funded by Grant-in-Aids for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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