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How to use SNPchiMp?

We have built this tool in order to be intuitive. We trust you'll be able to navigate its options without reading a tedious user manual (who has time for that these days anyway?!). However, if you're not finding something you need, or if the options are not clear enough, here you can download the user manual (pdf format).

 

What is SNPchiMp?

SNPchiMp v.3 is a free web-based tool that allows researchers to “jump” between different SNP chips and types of information in many species, in an intuitive and user friendly way.
With SNPchiMp v.3 you can, with a few clicks:

  • Know which SNPs are contained in all (or part of) commercial SNP chips currently available for the species considered (e.g. for imputation or data integration);
  • Get chromosome and physical position of your SNPs, updated to the any genome assembly you like.
  • Have your commercial SNP/probe names linked to a [rs/ss]IDs.
  • Have complete access to sender original information, including orientation, strand, etc. (e.g. for integration of your data with full sequence).
  • Obtain direct access to Illumina’s FORWARD/REVERSE or TOP/BOT allele coding customized to the desired SNP chip(s).
  • Obtain the latest version of the Interbull SNP exchange index. 
  • Browse your genomic analyses results: explore your results directly, link your SNPs to dbSNP and ENSEMBL.
  • Interact with Ensembl BioMart and Variant Effect Predictor (VeP) tools directly (query and download your results without any extra work!).
  • Access the open-source (or open-access for third parties) tools for basic SNP data management (like SNP allele conversion) provided in the "Tools" section.

 

Why using SNPchiMp?

  • Because there are two main SNP array producers and many custom SNP chips available that have different output data options.
  • Because higher density SNP chips do not contain all the SNPs in the lower density chips.
  • Because some SNPs have been referenced with different SNP names within the same community.
  • Because there are and there will be updates in the reference assembly, especially for species with a recent reference genome!
  • Because it is hard to find the links between commertial SNP names and rsIDs (that are often searchable terms in all public DBs).
  • Because SNP alleles in output files are difficult to handle (e.g. A/B, FORWARD, TOP)
  • Because for some downstream analyses, knowing the strand of the SNPs (with respect to the reference genome) can be fundamental. 
  • Because with SNPchiMp you can have access to Biomart directly and extract all the genes annotated within a user-defined range up-/down-stream of your SNPs. In addition you can extract the consequence of your subset of mutations using Ensembl VeP API REST tool, now integrated entirely in the tool!

 

How to cite SNPchiMp?

If you find this tool useful and use it for your research, please cite:

Nicolazzi E.L., Caprera A., Nazzicari N., Cozzi P., Strozzi F., Lawley C., Pirani A., Soans C., Brew F., Jorjani H., Evans G., Simpson B., Tosser-Klopp G., Brauning R., Williams J.L., Stella A. (2015). SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species. BMC genomics, 16:283

 

If you used older versions of SNPchimp on your work, you can also cite:

Nicolazzi E.L., Nazzicari N., Caprera A., Fojadelli I., Strozzi F., Schnabel R.D., Lawley C., Pirani A., Brew F., Soans C., Jorjani H., Evans G., Simpson G., Williams J.L., Stella A. (2014). SNPchiMp v.2: An Open Access Web Tool for SNP Data Management on Bovine, Procine and Equine Livestock. Proceedings of the 10th World Congress of Genetics Applied to Livestock Production. Vancouver (BC), Canada. 17-22 August 2014. 

 

Nicolazzi E.L., Picciolini M., Strozzi F., Schnabel R.D., Lawley C., Pirani A., Brew F. and Stella A. (2014) SNPchiMp: A database to disentangle the SNPchip jungle in bovine livestock. BMC genomics, 15:123

 

 

 

 

 

 

Disclaimer 
Copyright © 2014 Nicolazzi EL, Nazzicari N, Caprera A, Cozzi P, Strozzi F, Stella A. SNPchiMp is a free web-tool that uses open databases and information that is publicly available online: you can redistribute it and/or modify the information you download, but at your own risk. SNPchiMp v.3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details: https://www.gnu.org/licenses/. Some of the authors of this tool were funded by Gene2farm project, which was financed with support from the European Commission. However, the European Commitssion nor the partners of the project can be held responsible for any information contained in this website. Images in Download and Browse menus where found over the internet in random websites such as: webweaver.nu, bestclipartblog.com, staceyreid.com.

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