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MIPgen specifications


Unique identifier OMICS_04657
Name MIPgen
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++, Python
Computer skills Advanced
Version 1.1-14
Stability Stable
Source code URL https://codeload.github.com/shendurelab/MIPGEN/legacy.tar.gz/master
Maintained Yes



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  • person_outline Jay Shendure <>
  • person_outline Evan Boyle <>

Publication for MIPgen

MIPgen in publications

PMCID: 5935718
PMID: 29728634
DOI: 10.1038/s41598-018-25328-5

[…] sequences) with ligation and extension probes localized on different exons, depending on the splice variant to be detected, and leaving a gap of maximum 112 nt. smmips were designed based on the mipgen algorithm as described by boyle et al. and added to a large panel of previously designed smmips. the panel of phosphorylated smmips was hybridized to cdna after which the gap was filled […]

PMCID: 5770625
PMID: 29375588
DOI: 10.3389/fpls.2017.02016

[…] the successful detection of fusarium oxysporum f.sp. conglutinans in infected arabidopsis thaliana with a detection limit of 2.5 ng (). in order to improve the efficiency of mip assays, the mipgen software has been developed for the design and performance prediction of individual mips ()., serious limitations of these assays are the requirement for several temperature settings […]

PMCID: 5595890
PMID: 28900252
DOI: 10.1038/s41598-017-11035-0

[…] manner to a cdna of interest, followed by gap-filling/ligation and pcr. smmips against the antisense strand of 104 predicted transcripts (ucsc human genome assembly hg19) were designed based on the mipgen algorithm as described by boyle et al.. whenever possible, smmips were designed with ligation and extension probes located on adjacent exons to prevent contribution of smmip probes […]

PMCID: 5685235
PMID: 28572161
DOI: 10.3324/haematol.2017.169136

[…] table s2), identifying polymorphisms carried in cell lines, and other clinically relevant genes (abl1, alk, jak2, nt5c2, and ros1) using the program molecular interaction potential generator (mipgen). as detailed in the online supplementary methods, 500 ng genomic dna was hybridized with the panel, exonuclease-treated, and pcr-amplified to generate sequencing libraries. single libraries […]

PMCID: 5539915
PMID: 28628100
DOI: 10.1038/nn.4589

[…] test for testing the enrichment of specific gene sets, including neuronal compartments such as the post-synaptic density and targets of chd8 and fmrp in brain tissue., smmips were designed with the mipgen program to capture sequences of interest. to maximize coverage, we designed one smmip for each strand for each target. we first used smmips targeting 24 sites to sequence eight cohorts […]

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MIPgen institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
MIPgen funding source(s)
Supported by a grant from the National Cancer Institute (CA160080).

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