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Pseudomarker specifications


Unique identifier OMICS_07100
Name Pseudomarker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained No


No version available


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Publication for Pseudomarker

Pseudomarker citations


Metabolic QTL Analysis Links Chloroquine Resistance in Plasmodium falciparum to Impaired Hemoglobin Catabolism

PLoS Genet
PMCID: 3879234
PMID: 24391526
DOI: 10.1371/journal.pgen.1004085
call_split See protocol

[…] Genome-wide scans were performed using pseudomarker to detect QTLs associated with metabolite levels in the HB3×Dd2 genetic cross. Intensities of mass signals were log-transformed and the median signal for each mass across replicates was […]


Fine Scale Mapping of Natural Variation in Fly Fecundity Identifies Neuronal Domain of Expression and Function of an Aquaporin

PLoS Genet
PMCID: 3320613
PMID: 22509142
DOI: 10.1371/journal.pgen.1002631

[…] nsformed to produce estimates of total fecundity.QTL mapping was performed with estimates of total fecundity for each RIL (see for details) using multiple imputation with 50 imputations per marker/pseudomarker and a pseudomarker step size of 3cM. We tested for association between genomic location and fecundity by fitting the full model, y = Mi+E+Mi:E+ε, and the reduced model, y = E+ε, where y i […]


The landscape of inherited and de novo copy number variants in a plasmodium falciparum genetic cross

BMC Genomics
PMCID: 3191341
PMID: 21936954
DOI: 10.1186/1471-2164-12-457

[…] geny, QTL associated with the probe will be localized with the respective MS marker position in the linkage map. QTL analysis was carried out by computational approaches described previously [] using Pseudomarker (Version 2.04, A high significance threshold (LOD ≥ 5) as well as lower LOD thresholds of LOD ≥ 3 and LOD ≥ 2 was used for Q […]


Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits

PMCID: 3170002
PMID: 21918629
DOI: 10.2147/AABC.S9240

[…] que, is rather extensive and is not shown here. If the marker interval is very short we fit only a one-degree polynomial to the endpoint data, and if the marker interval is unusually long we insert a pseudomarker with no genotype information at the midpoint. The polynomial fitting is done in a preparation step. In the optimization algorithm, the matrix A(x) needs to be computed for a given locatio […]


Structural Model Analysis of Multiple Quantitative Traits

PLoS Genet
PMCID: 1513264
PMID: 16848643
DOI: 10.1371/journal.pgen.0020114

[…] Genome scans were carried out in the MATLAB software environment (MathWorks, Natick, Massachusetts, United States) using the pseudomarker package (v2.02) []. Scans were conducted at 2 cM resolution using the imputation method with 256 imputations. Significance of QTLs was assessed using permutation analysis [] with 1,000 pe […]


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Pseudomarker institution(s)
The Jackson Laboratory, Bar Harbor, ME, USA

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