Tools
Tools and Data constructed by our lab:
- SERV - "Sequence-Based Estimation of Repeat Variability". A tool to find tandem repeats in DNA sequences and estimate the variability of each repeat found. The higher the VARscore, the higher the estimated variability. Sequences with VARscores above 1 are usually polymorphic between species/strains.
For more information, see: Legendre, M., Pochet, N., Pak, T. and Verstrepen, K.J. (2007). Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Research. PDF file.
- Searchable Databases containing all tandem repeats located within genes and/or promoters of the following organisms: S. cerevisiae, A. thaliana, O. sativa, A. fumigatus.
- Excel file containing the top 100 most variable repeats (predicted using SERV) located within human coding sequences (exons). PDF file of relevant paper on the SERV algorithm.
- PDF File containing all S. cerevisiae Open Reading Frames (ORFs) containing "non-fuzzy" internal tandem repeats. Reference: Verstrepen et al., Nature Genetics 37: 986-990 (2005). PDF file of this paper.
- Excel files with raw data and enrichment analysis of genome-wide expression data of FLO1-expressing versus flo1 cells.
Protocols:
- High-yield total RNA isolation from S. cerevisiae. (download PDF)
- A simple yet efficient protocol for yeast transformation. Works fine with industrial strains as well. (download PDF)
- Quick genomic prep from yeast. This prep yields semi-pure gDNA, perfect for diagnostic PCR. (download PDF)
- RNA prep from yeast cells using the ABI6100 Nucleoprep machine. (download PDF)
Links:
- Dot Plots - find repeats in a DNA sequence, or duplicated areas in two sequences.
- Compare Two Excel Lists - handy program developed by the Whitehead Institute’s BARC team to compare two excel columns and find which elements are common and unique to each list.
- OSPREY - automated visualization of gene/protein interaction networks.
