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Publicly available Project data

Mouse SNP haplotype Viewer

Link to example of SNP haplotype  Viewer

Displays graphical representations of SNP and haplotypes of C57BL/6, A/J, BALB/CBYJ, 129S1/SvImJ and C3H/HeJ for any region of the mouse genome based on Perelgen SNP. Additional data for Mmu17 30637692 to 36837814 (NCBI37) is from our own resequencing. Tables of data underlying all displays can be downloaded. A full description of the methods and conclusions are provided in:

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Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background Harry A Noyes, Morris Agaba, Susan Anderson, Alan L Archibald, Andy Brass, John Gibson, Laurence Hall, Helen Hulme, Sung Jong Oh and Stephen Kemp BMC Genomics 2010;11:361


Viewer for mouse and cow microarray data

Link to Gene Expression Viewer

The Gene Expression Viewer displays plots of gene expression in the liver and spleen of A/J, BALB/c and C57BL/6 before infection with Trypanosoma congolense and at days 3, 7, 9 and 17 after infection. Data for days 0 and 7 is available for the kidney. Data was collected using the Affymetrix 430_2 expression arrays see Noyes et al 2009 Mechanisms controlling anaemia in Trypanosoma congolense infected mice for details of sample collection and data analysis. (The viewer Requires Firefox or Safari; does not function with InternetExplorer. This is not deliberate but it is a long way down my list of bugs to fix)


Select from 271,981 Cape Buffalo (Syncerus caffer) SNP

Subsets of 271,981 SNP that are polymorphic in Cape Buffalo and that meet a range of criteria can be downloaded. This Primer Design Programme can be used to design primers to amplify selected SNP loci. SNP can also be selected that disrupt an enzyme restriction site for design of PCR-RFLP assays.

Design primers for PCR-RFLP for the Illumina Bovine 55k SNP set

This Primer Design Programme is for design of primers to amplify loci included in the Illumina Bovine SNP50 set of 55,000 bovine SNP. SNP can be selected that disrupt an enzyme restriction site for design of PCR-RFLP assays.

Design primers for PCR-RFLP for the Perlegen 8 million Mouse SNP set

This Primer Design Programme is for design of primers to amplify loci included in the Perlegen Mouse SNP set of 8 million SNP. SNP can be selected that disrupt an enzyme restriction site for design of PCR-RFLP assays. The page can take a moment or two to load, please be patient.

Primer Design Programme

This Primer Design Programme allows the design of a single primer against each sequence in a file or to design multiple primer pairs tiling across a single sequence.


Recombination Break Point Distribution programme

Recombinant Link image

The Recombination Break Point Distribution programme produces a table of the mean and standard deviation of haplotype sizes after a user specified number of generations of mating between a user specified number of founder. Graphics of examples are generated and tables of data can be downloaded from which plots of the distribution can be created in Excel.


Microsatellite Locus Extractor Programme

The Microsatellite Locus Extractor Programme extracts microsatellite loci and flanking sequence from public genome sequences and returns them in a form suitable for input into the The Primer Design Programme (above). This makes it easy to design microsatellite markers for any of the following organisms: Anopheles gambiae P3, Drosophila BDGP4, Bos taurus Bta2 and Bta3, C. elegans 150, Mouse NCBI36, Zebra Fish 6, Leishmania major V5, Leishmania infantum V3 and Leishmania braziliensis V2.


Dungfly SNP database

Yellow dungfly courtesy of Prof Paul F. Brain  University of Wales,Swansea

Dungfly SNP data base: ScataSNP A database of SNP in dungfly (Scatophagia stercoraria) obtained by Dr Derek Daly by partial sequencing of a pool of DNA from 10 dungflies on a Roche 454 sequencer


Demo Perl script for obtaining SNP annotation from Ensembl API

This Perl Script (7.5Mb) demonstrates how to obtain SNP annotation from the Ensembl API. It contains instructions for use and the Ensembl API code but does require a functioning MySQL installation. It is useful for demonstration purposes but can also be adapted to obtain annotation for thousands of SNP for genomes supported by Ensembl