tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

Marker2sequence

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.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible

0 user reviews

0 user reviews

No review has been posted.

Marker2sequence forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.

No open topic.

Marker2sequence versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.

No versioning.

Marker2sequence classification

  • Plants

Marker2sequence specifications

Software type:
Package/Module
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
Operating system:
Unix/Linux
License:
Apache License version 2.0
Stability:
Stable
Source code URL:
https://github.com/PBR/Marker2Sequence.git
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
Programming languages:
Java
Computer skills:
Advanced
Maintained:
Yes

Marker2sequence support

Maintainer

  • Richard Finkers <>

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.

Publications

Institution(s)

Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, Netherlands; Graduate School Experimental Plant Science, Wageningen, Netherlands; Centre for Biosystems Genomics, Wageningen, 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

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.