McClintock protocols

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McClintock specifications

Information


Unique identifier OMICS_14560
Name McClintock
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A reference genome, a consensus set of TE sequences and a paired end sequencing read.
Input format FASTA, FASTQC
Output format BED
Operating system Unix/Linux, Mac OS
Programming languages Java, Perl
Computer skills Advanced
Stability Stable
Requirements
FASTQC, RepeatMasker, R, BWA, BioPerl, SAMtools, Blat, Bowtie, BEDTools, twoBitToFa, BCFTools, Exonerate
Maintained Yes

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  • person_outline Casey Bergman <>

Publication for McClintock

McClintock in pipelines

 (2)
2017
PMCID: 5737362
PMID: 28985298
DOI: 10.1093/gbe/evx170

[…] 2017. easy configuration and the modular architecture make it convenient to adapt teddypi to process data from a broad range of te/sv callers or other integration pipelines such as svmerge or mcclintock (; ). teddypi can be applied to any group of organisms where accurate te/sv calling is feasible., whole genome sequencing data generated with illumina hiseq technology from and miller et […]

2013
PMCID: 3615998
PMID: 23573266
DOI: 10.1371/journal.pone.0060551

[…] for pargir93a, ay098942.1 for hameir25a, nm_135019.2 for dmelir25a, nm_167185.1 for dmelir8a, and nm_142666.4 for dmelir93a. the hameir8a sequence is unpublished (generously shared by dr. timothy mcclintock)., structural analysis and alignment of the spiny lobster ir25a and ir8a predicted amino acid sequences reveals that they have a predicted protein structure similar to that of iglurs […]


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McClintock in publications

 (435)
library_books

Reviewer List

PMCID: 5932474
DOI: 10.1093/ijnp/pyy039

[…] magalhaes, pedro, majdandzic, jasminka, maldonado-vlaar, carmen, malhotra, anil, mantsch, john, marin, marcelo, mathe, aleksander, mathew, sanjay, mathews, douglas, matsuo, koji, mavrikaki, maria, mcclintock, shawn, mccusker, robert, mcguire, philip, mechawar, naguib, mehta, divya, mehta, mitul, meyer, jeff, meyerhoff, dieter j., mier, daniela, miguel-hidalgo, jose javier, mizrahi, romina, […]

PMCID: 5930866
PMID: 29743957
DOI: 10.1186/s13100-018-0120-9

[…] rich biology of repetitive and mobile dna. in this article, i present four arguments supporting a case for retaining repetitive dna in your genome-wide analysis., from the time of their discovery by mcclintock, transposable elements (tes) have had a history of being ignored []. termed “controlling elements” by mcclintock for their roles in developmental regulation, tes were first disregarded, […]

PMCID: 5915539
PMID: 29720985
DOI: 10.3389/fpls.2018.00429

[…] crosses between triploid and diploid maize plants resulted in aneuploid offspring with differing chromosome numbers and insufficient phenotype compared to the diploid and triploid parental plants (mcclintock, ). in contrast to maize, cross experiments of triploid and tetraploid rose plants indicated that triploid roses were able to produce haploid and diploid male and female gametes (van […]

PMCID: 5938444
PMID: 29760907
DOI: 10.1002/ece3.4023

[…] to detect all individuals present. rates of detection can also be influenced by variation among observers, with less‐skilled observers being more likely to miss or falsely identify an organism (mcclintock, bailey, pollock, & simons, ). with such a diverse set of causes, it can easily be understood that imperfect detection is prevalent among ecological studies. unfortunately, this issue […]

PMCID: 5896891
PMID: 29649213
DOI: 10.1371/journal.pgen.1007282

[…] one year of laboratory culture, suggesting that is6110 transposition is dynamically adapted to the host and to adverse growth conditions., since the pioneering discovery of transposition by barbara mcclintock in eukaryotes and later in prokaryotes by robert w. hedges and alan e. jacob, it has become clear the key role of mobile genetics elements in chromosome remodelling, microbial evolution […]


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McClintock institution(s)
Faculty of Life Sciences, University of Manchester, Manchester, UK; Centro de Biotecnologia e Química Fina (CBQF), Universidade Católica Portuguesa, Porto, PT; Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
McClintock funding source(s)
This work was supported by Wellcome Trust Award 096602/B/11/Z.

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