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Pseudomarker specifications

Information


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

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for Pseudomarker

Pseudomarker citations

 (5)
call_split

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

2014
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 […]

library_books

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

2012
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 […]

library_books

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

2011
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, http://churchill.jax.org/software/archive/pseudomarker.shtml). A high significance threshold (LOD ≥ 5) as well as lower LOD thresholds of LOD ≥ 3 and LOD ≥ 2 was used for Q […]

library_books

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

2010
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 […]

library_books

Structural Model Analysis of Multiple Quantitative Traits

2006
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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