Mitofy protocols

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Mitofy specifications

Information


Unique identifier OMICS_19237
Name Mitofy
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Andrew Alverson <>
  • person_outline Douglas Senalik <>

Information


Unique identifier OMICS_19237
Name Mitofy
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Andrew Alverson <>
  • person_outline Douglas Senalik <>

Publication for Mitofy

Mitofy in pipelines

 (7)
2018
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] 7 single lines (837,015 bp)., the assembled contigs were firstly annotated by ncbi-blastn based on the local database with an e-value < 1e−6. then, the boundaries of each gene were confirmed by mitofy and exported as sequin formatted files. trna genes were further predicted by trnascan (http://lowelab.ucsc.edu/trnascan-se/)(supplementary table )., the paired-end reads for protocorm, […]

2017
PMCID: 5374973
PMID: 28367378
DOI: 10.7717/peerj.3148

[…] mistakes generated by 454 gs flx titanium platform (especially in a/t enriched regions). finally, the complete mt genome sequence of s. suchowensis was finished., the web-based tool public mitofy analysis was used to identify genes (), accompanying with synonymous and none-synonymous snps. we also revised the start and stop codons of genes by learning similar genes, […]

2016
PMCID: 4842374
PMID: 27148547
DOI: 10.1155/2016/5283628

[…] the reads, which were partly overlapped (≥95% identical, e ≤ 1e − 30) with the contigs. finally, a 255,773 bp nucleotide sequence was finished., genes were located using the web-based tool public mitofy analysis [], coupled with synonymous and nonsynonymous snps. trnascan-se was used to identify the transfer rna genes with default settings []. gc content was analyzed by perl script. […]

2016
PMCID: 5026442
PMID: 27635002
DOI: 10.1128/genomeA.00981-16

[…] the de novo assembly was digested in silico and aligned () to a previously published restriction map (). the genome was finished by hand using illumina and roche 454 reads and annotated using the mitofy software ()., the genome’s master replication circle is 300,945 bp in length with a g+c content of 45%. it includes a large repeat 12,933 bp in length and two single-copy regions, measuring […]

2015
PMCID: 4540028
PMID: 26290780
DOI: 10.7717/peerj.1066

[…] () and assembled separately using velvet (). gene prediction and assembly of chloroplast genome was done using dogma (). gene prediction and annotation of the mitochondrial assembly was done using mitofy ()., we aligned neem contigs on citrus (citrus sinensis) chromosomes using mummer program (). synteny was computed among neem and citrus using symap4.0 (). the synteny information […]

Mitofy in publications

 (11)
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] 7 single lines (837,015 bp)., the assembled contigs were firstly annotated by ncbi-blastn based on the local database with an e-value < 1e−6. then, the boundaries of each gene were confirmed by mitofy and exported as sequin formatted files. trna genes were further predicted by trnascan (http://lowelab.ucsc.edu/trnascan-se/)(supplementary table )., the paired-end reads for protocorm, […]

PMCID: 5374973
PMID: 28367378
DOI: 10.7717/peerj.3148

[…] mistakes generated by 454 gs flx titanium platform (especially in a/t enriched regions). finally, the complete mt genome sequence of s. suchowensis was finished., the web-based tool public mitofy analysis was used to identify genes (), accompanying with synonymous and none-synonymous snps. we also revised the start and stop codons of genes by learning similar genes, […]

PMCID: 5078923
PMID: 27776481
DOI: 10.1186/s12864-016-3159-3

[…] from h602 and haruna nijo were mapped and aligned onto the reference mitochondrial draft genome of h602., the genes encoding mitochondrial proteins and rrnas were identified using blastn and mitofy [] based on the known annotation of the mitochondrial genes of wheat cv. chinese spring []. the trnascan-se 1.21 server [] was used to identify trnas. repeat sequences (>100 bp and >80 % […]

PMCID: 4842374
PMID: 27148547
DOI: 10.1155/2016/5283628

[…] map (). finally, the t. parvula single master circle of mitochondrial genome covering the great mass of the contigs was generated with a complete length of 255773 bp., using web-based tool public mitofy analysis [] and trna scan-se, 54 genes were identified, including 3 ribosomal rna (rrna) genes (5s rrna, 26s rrna, and rrns), 19 transfer rna (trna) genes, and 32 protein-coding genes (pcgs) […]

PMCID: 4599086
PMID: 26450727
DOI: 10.1128/genomeA.01151-15

[…] a paired-end approach with a read size of ~100 bp was employed. sequence assembly was performed with soapdenovo2 software version 2.01 (). all open reading frames were annotated using cpgavas () and mitofy () for chloroplast and mitochondrial genomes, respectively., the p. crispa plastid genome (cpdna) information resides on a single molecule with a total length of 196,502 bp and a g+c content […]

Mitofy institution(s)
Department of Biology, Indiana University, Bloomington, IN, USA; Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY, USA; DOE Joint Genome Institute, Walnut Creek, CA, USA
Mitofy funding source(s)
Supported by a National Institutes of Health (NIH) Ruth L. Kirschstein National Research Service Award Postdoctoral Fellowship (1F32GM080079-01A1), an NIH research grant RO1-GM-70612, the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc., the US Department of Energy’s Office of Science, Biological and Environmental Research Program, the University of California, Lawrence Berkeley National Laboratory under contract no. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract no. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract no. DEAC02-06NA25396.

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