6) Development of software for the management and analysis of DNA sequences

We are developing software for handling large amounts of genetic data with ease.

1) Do you have a complex pattern of consensus sequences (Example: CCYRY--[20 to 30 base pairs]--GRRYYRR) ? We created COMPASSS (complex pattern of sequences search software).

    With COMPASSS, developed by Dr. Giuseppe Maccari (first public release, beta testing) you can find where complex motives are, at genome-wide level, for all the organisms available in genebank. You can find more homologies than ever . A manuscript, under submission, will show some applications. Free download COMPASSS here. Tutorial also on YouTube here. No installation is required: simply unzip into a new folder and run the executive.

Tutorial of COMPASSS

2) A bundle developed by Luca Pandolfini, called PHASEVIEW, is another simple software helping the haplotype reconstruction from individual genotypes. Genotypes are entered in the proper format into an Excel worksheet. PHASEVIEW automatically reconstruct individual genotypes by using fastPHASE (Scheet, P. and M. Stephens (2006). A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78, 629–644.), then, automatically, open HaploView (Barrett J.C., Fry B., Maller J., Daly M.J. (2005). "Haploview: analysis and visualization of LD and haplotype maps". Bioinformatics 21: 263–265. doi:10.1093/bioinformatics/bth457. PMID 15297300) to show the results. JAVA, HaploView, and ActivePERL need to be installed already on the local PC. Free download PHASEVIEW here.

3) A third software [in preparation by Dr. Giuseppe Maccari] will allow to handle virtually all the SNPs of the genomes and will help to select only those meeting specific criteria, narrowing your hypotheses in genetic studies.

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