Mitofy pipeline

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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Documentation


Maintainers


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

Publication for Mitofy

Mitofy IN pipelines

 (2)
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 43)., the paired-end reads for protocorm, […]

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

[…] the de novo assembly was digested in silico and aligned (9) to a previously published restriction map (10). the genome was finished by hand using illumina and roche 454 reads and annotated using the mitofy software (11)., 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 […]

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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