QGene protocols

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QGene specifications

Information


Unique identifier OMICS_12660
Name QGene
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Input format .qdf
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Version 4.3.10
Stability Stable
Maintained Yes

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Maintainer


  • person_outline QGene Team <>

Publications for QGene

QGene in pipelines

 (2)
2012
PMCID: 3504571
PMID: 23043321
DOI: 10.1186/1471-2156-13-84

[…] of the linkage groups (lgs) and the qtls were obtained using mapchart version 2.2 []. pleiotropy of co-localized qtls was tested by multiple trait multiple interval mapping (mmim) function of the qgene 4.3.8 software []., blast: basic local alignment search tool; cm: centimorgan; est: expressed sequence tag; est-ssr: an ssr obtained from a cdna sequence located in est; estp: expressed […]

2011
PMCID: 3044735
PMID: 21390308
DOI: 10.1371/journal.pone.0017327

[…] carried out on a roche lightcycler 480 using brain cdna, a sybr green i pcr mix (roche) and the same primers listed above for mapping the deletional breakpoint. data analysis was performed with the qgene software and the expression results normalized to or51a1p., membrane topology of the six ors was predicted using a web-based algorithm (http://www.cbs.dtu.dk/services/tmhmm/) and a stand […]


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QGene in publications

 (115)
PMCID: 5880813
PMID: 29619232
DOI: 10.1038/s41438-018-0022-5

[…] dna was extracted from fresh tissue of each head with the qiagen dneasy plant mini kit (qiagen, valencia, ca, usa)., qtl mapping on both populations (s88 × lb and pav × par) was performed with qgene v. 4.3.9 software using a scan interval of 1 cm and the single-trait, multiple interval mapping (smim) approach. the threshold for significant qtls was set at the genome-wide α = 0.05 […]

PMCID: 5800283
PMID: 29402302
DOI: 10.1186/s13104-018-3202-3

[…] qtl controlling salt tolerance was identified by single-marker regression (smr), single trait composite interval mapping (cim), and single trait multiple interval mapping (mim) analyses using qgene 4.3.10 []. qtl lod levels higher than 2.5 were significant. the lod plots were created by mapchat 2.2 [] based on the data from qtxb20 and qgene., ‘jidou 12’ showed significantly (p ≤ 0.01) […]

PMCID: 5776780
PMID: 29357813
DOI: 10.1186/s12864-018-4438-y

[…] for qtl analysis. the shapiro-wilk test was used to determine the normality of the population data. all statistical tests were performed using r version 3.3.2 []. qtl analysis was conducted using qgene version 4.4.0 []. traits were analyzed using a multiple interval mapping algorithm based on a general linearized framework (mim-glz) []. significant qtls (α = 0.05) were identified using […]

PMCID: 5778143
PMID: 29403518
DOI: 10.3389/fpls.2018.00008

[…] 6b). the map length spanned 2,119.2 cm, as 965.5 cm for the a genome, and 1,153.7 cm for the b genome., qtl analysis was performed using the composite interval mapping method (zeng, ) with the qgene software, version 4.3.10 (joehanes and nelson, ). a simplified, but representative, version of the linkage map with a total of 1,627 non-co-mapping markers was used to speed up the computation […]

PMCID: 5793172
PMID: 29304028
DOI: 10.3390/genes9010019

[…] at least 99% identity and 100% query coverage) against the chinese spring (cs) survey sequence data using ncbi standalone blast program []. , software packages qtl cartographer (version 1.6) [,] and qgene (version 4.3.10) [] were used for mapping main effect qtl (m-qtl) separately for each environment using composite interval mapping method with mapping function kosambi [] and regression method […]


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QGene institution(s)
Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
QGene funding source(s)
Support has been provided by National Science Foundation NSF-DBI grant 0109879 and USDA-NRI Applied Plant Genomics Program grant 2004-35317-14867 entitled ‘RiceCAP: A coordinated research, education, and extension project for the application of genomic discoveries to improve rice in the United States’. This is contribution 09-111-J from the Kansas Agriculture Experiment Station.

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