GenomeMatcher pipeline

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

 (5)
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.24 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.25 […]

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

[…] genome synteny plot of the chromosomes of the two strains was drawn using genomematcher.24 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.25 homology searches were preformed using blast+.26 the phylogenetic tree was prepared using figtree […]

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 (33) using the program genomematcher (21) 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 […]

2012
PMCID: 3759362
PMID: 22863735
DOI: 10.1038/ng.2375

[…] a total of 1,264 aligned contigs were validated by mapping paired-end reads from fosmid clones using blastn (e-value: <1e-15, identity: >90%, coverage: >200bp) implemented in the software genomematcher version 1.6528. additional linkages (699 regions) were made using pcr across the intervening sequence gaps with primers designed from neighboring contigs. length of sequence gaps […]

2009
PMCID: 2745422
PMID: 19703286
DOI: 10.1186/1471-2164-10-395

[…] to the data available from genbank accession achu00000000, the velvet assembly and predicted protein sequences are provided in fasta format in additional files 6 and additional file 7., we used genomematcher [78] for generating and visualising whole-genome alignments. for aligning short illumina sequence reads against a reference genome, we used maq [79] and for other sequence alignments […]

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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