Marker Mining

A combination of in-house scripts and publicly available software applications have been developed to mine SSRs and SNPs from Sanger-style or next generation sequence sets.

SNPs
Preferably, starting sequences have been trimmed and filtered for low quality. For SNPs, an assembly of the sequences is also needed, and software is run to statistically differentiate insertion/deletion and substitution events from random sequencing errors. The results are provided in a ranking from the most to least likely SNPs to be truly polymorphic. CUGI's bioinformatics core has experience filtering and formatting SNPs for inclusion on custom SNP microarray chips.

SSRs
SSRs are discovered as patterns of dinucleotides with at least five repeats, trinucleotides with at least four repeats, and tetra-, penta- and hexanucleotides with at least three repeats (although these parameters can be adjusted as needed for the project). Further analysis can be performed to examine sequence assemblies for underlying evidence of polymorphism within the gene set. Forward and reverse primers for SSRs and SNPs are automatically generated. Results are provided in Excel spreadsheets.

All bioinformatic services are charged at an hourly rate, and rates are constructed to recover costs for equipment, service contracts and labor, and do not reflect labor alone. Please contact CUGI for an exact quote for a project.

Cost: 
Clemson or Federal Agency: $110.00, per hour
Non-profit or Academic: $115.00, per hour
Commercial: $175.00, per hour