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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 citations

 (49)
library_books

Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis

2017
Genome Biol Evol
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 […]

library_books

Genomic Characteristics of Bifidobacterium thermacidophilum Pig Isolates and Wild Boar Isolates Reveal the Unique Presence of a Putative Mobile Genetic Element with tetW for Pig Farm Isolates

2017
Front Microbiol
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. […]

library_books

Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture

2017
Sci Rep
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 […]

call_split

Characterization of the genuine type 2 chromatic acclimation in the two Geminocystis cyanobacteria

2017
PMCID: 5737509
PMID: 28338901
DOI: 10.1093/dnares/dsx011
call_split See protocol

[…] 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 […]

library_books

Complete Genome Sequence of Bradyrhizobium diazoefficiens USDA 122, a Nitrogen Fixing Soybean Symbiont

2017
Genome Announc
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. […]

library_books

Complete Genome Sequence of Bradyrhizobium japonicum J5, Isolated from a Soybean Nodule in Hokkaido, Japan

2017
Genome Announc
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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