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MICADo specifications

Information


Unique identifier OMICS_27043
Name MICADo
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data The reference sequences for a gene of interest and several read sets corresponding to the gene panel sequencing of a cohort of patients.
Input format FASTQ+FASTA/TSV
Output format JSON,TSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
scipy, appnope, biopython, decorator, gnureadline, ipython, ipython-genutils, msgpack-python, networkx, numexpr, numpy, pandas, path.py, pexpect, pickleshare, ptyprocess, pyparsing, python-dateutil, pytz, simplegeneric, six, traitlets, wsgiref, simplejson, python-Levenshtein, sklearn
Maintained Yes

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Documentation


Maintainers


  • person_outline Justine Rudewicz <>
  • person_outline Hayssam Soueidan <>
  • person_outline Macha Nikolski <>

Publication for MICADo

library_books

MICADo - Looking for Mutations in Targeted PacBio Cancer Data: An Alignment-Free Method.

2016 Front Genet
PMCID: 5143680
PMID: 28008336
DOI: 10.3389/fgene.2016.00214

MICADo in publications

 (11)
PMCID: 5904483
PMID: 29674892
DOI: 10.3897/zookeys.740.22654

[…] flavoniger giordani soika, 1941, eumenes labiatus labiatus giordani soika, 1941, eumenes labiatus sinicus giordani soika, 1941, eumenes mediterraneus manchurianus giordani soika, 1971, eumenes micado cameron, 1904 (kim and yoon (2001) state that the record is very doubtful), eumenes multipictus de saussure, 1855, eumenes nigriscutatus zhou, chen & li, 2012, eumenes pedunculatus […]

PMCID: 5772046
PMID: 29343757
DOI: 10.1038/s41598-017-17463-2

[…] figure s7 was drawn by d.k. p.e.g. advised the structuring of the manuscript and contributed to the writing. the general design of the wood fall experiments was also discussed under the micado project (jcjc anr-11jsv7-003-01) supervised by p.e.g. all authors contributed to the implementation of the experiments., the authors declare that they have no competing […]

PMCID: 4992311
PMID: 27542896
DOI: 10.1186/s12866-016-0807-3

[…] locus while creating a lacz fusion (strain bfs815) was done within the framework of a european project on the functional analysis of the genome of b. subtilis (see http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi)., plasmid pac6 [] allowed the construction of a transcriptional fusion between the promoter region of yvmb (nucleotides −291 to +9 relative to the translational start site) […]

PMCID: 4848640
PMID: 27096870
DOI: 10.3390/toxins8040114

[…] toxins with 40–60 amino acids and three to four disulfide bonds. therefore, pmtxs may also be useful for research tools and drug discovery [,,,,,]., the eumenine wasp anterhynchium flavomarginatum micado may be the most common solitary wasp in japan, hunting only green caterpillars and building their nests in bamboo twigs with mud. the major component of this venom, eumenine mastoparan-af […]

PMCID: 3554493
PMID: 23324196
DOI: 10.1186/1746-4269-9-7

[…] jagang province (for which he entered “bees”) and the province to the south of pyongyang known as north hwanghae (for which he entered “locust” and the orthopterans “acrida turrita and gompsocleis micado”). such uses, however, were unknown to my students., however, my pyongyang student informants all knew that silkworm caterpillars and pupae can be eaten and reported that some people will eat […]


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MICADo institution(s)
Centre de BioInformatique de Bordeaux, University of Bordeaux, Bordeaux, France; Laboratoire Bordelais de Recherche en Informatique, Centre National de la Recherche Scientifique, University of Bordeaux, Bordeaux, France; Bergonié Cancer Institute, Institut National de la Santé et de la Recherche Médicale U1218, University of Bordeaux, Bordeaux, France; Karolinska Institute and University Hospital, Stockholm, Sweden
MICADo funding source(s)
Supported in part by the SIRIC BRIO; by grants from the Swedish Cancer Society, Knut and Alice Wallenberg’s fund, the research funds at Radiumhemmet, Karolinska Institutet and Stockholm County Council, BRECT and ALF.

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