HaploPainter is a user-friendly pedigree-drawing application with special features for easy visualization of complex haplotype information. It has been developed to facilitate gene mapping in Mendelian diseases in terms of fast and reliable definition of the smallest critical interval harbouring the underlying gene defect. HaploPainter is written in Perl and may be used for visualization of haplotypes calculated by any of the common linkage programs. With special features like haplotype compression or the ability of marker section cut-out it particularly addresses the requirements for viewing large haplotypes as obtained by using for genome scans high-density marker panels of many thousands of single nucleotide polymorphisms (SNPs).
The sequencing of genes is routinely performed by sequencing the exonic regions after PCR amplification. The steps for this are complex and time consuming. Firstly, genes are represented by different transcripts.
On the other hand variable sequences should, such SNPs and fragment length polymorphisms, be included in the primer search. In addition the cutting of large overlapping fragments into smaller pieces, or the combining of closely contiguous fragments into larger is time-consuming too. Gene Explorer automates these steps and generates PCR primers using Primer3plus.
As a database for sequences and annotations the ENSEMBL database is used. Besides entering a ENSEMBL ID or gene symbol, no additional information is needed.
In pharmacogenomic investigations of compound activity against cancer, the growth-inhibiting potential is usually measured in a quantitative fashion to enable computational analysis of compound efficacy linked to genomic markers. A widely used approach is to measure the half-maximal inhibitory concentration (IC50) where cell viability is reduced by 50%.