Aims at mining quantitative trait loci (QTLs) for candidate genes. Marker2sequence, for each gene, within the QTL region, uses data integration technology to integrate putative gene function with associated gene ontology terms, proteins, pathways and literature. As a typical QTL region easily contains several hundreds of genes, this gene list can then be further filtered using a keyword-based query on the aggregated annotations. Marker2sequence will help breeders to identify potential candidate genes for their traits of interest.

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Marker2sequence classification

  • Plants

Marker2sequence specifications

Software type:
Package
Restrictions to use:
None
Output data:
The alignment of the reference genetic map with the genomic information, a list of all genes in the specified region, their location and description, the markers within this region, the genetic map for the specified region
Programming languages:
Java
Computer skills:
Advanced
Interface:
Command line interface
Input data:
Genomic region using the format Chr:start..stop, two markers flanking the QTL region or a list of markers spanning the QTL region
Output format:
PDF
License:
Apache License version 2.0
Stability:
Stable
Source code URL:
https://github.com/PBR/Marker2Sequence.git

Publications

Marker2sequence support

Maintainer

Credits

Institution(s)

Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands; Graduate School Experimental Plant Science, Wageningen, The Netherlands; Centre for Biosystems Genomics, Wageningen, The Netherlands; Crop Bioinformatics, INRES, University of Bonn, Bonn, Germany

Funding source(s)

This project was co-financed by the sixth framework EU project ‘High Quality Solanaceous crops for consumers, processors and producers by exploration of Biodiversity’, contract number: FOOD-CT-2006-016214, Wageningen UR Plant Breeding and the Centre for BioSystems Genomics (CBSG) which is part of the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research.

Link to literature

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