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Abstract Consanguineous families affected with a recessive genetic disease caused by homozygotisation of a mutation offer a unique advantage for positional cloning of rare diseases. Homozygosity mapping of patient genotypes is a powerful technique for the identification of the genomic locus harbouring the causing mutation. This strategy relies on the observation that in these patients a large region spanning the disease locus is also homozygous with high probability. The high marker density in single nucleotide polymorphism (SNP) arrays is extremely advantageous for homozygosity mapping. We present KinSNP, a user-friendly software tool for homozygosity mapping using SNP arrays. The software searches for stretches of SNPs which are homozygous to the same allele in all ascertained sick individuals. User-specified parameters control the number of allowed genotyping 'errors' within homozygous blocks. Candidate disease regions are then reported in a detailed, coloured Excel file, along with genotypes of family members and healthy controls. An interactive genome browser has been included which shows homozygous blocks, individual genotypes, genes and further annotations along the chromosomes, with zooming and scrolling capabilities. The software has been used to identify the location of a mutated gene causing insensitivity to pain in a large Bedouin family. KinSNP is freely available from http://bioinfo.bgu.ac.il/bsu/software/kinSNP.

Photometric stereo methods seek to reconstruct the 3d shape of an object from motionless images obtained with varying illumination. Most existing methods solve a restricted problem where the physical reflectance model, such as Lambertian reflectance, is known in advance. In contrast, we do not restrict ourselves to a specific reflectance model. Instead, we offer a method that works on a wide variety of reflectances. Our approach uses a simple yet uncommonly used property of the problem— the sought after normals are points on a unit hemisphere. We present a novel embedding method that maps pixels to normals on the unit hemisphere. Our experiments demonstrate that this approach outperforms existing manifold learning methods for the task of hemisphere embedding. We further show successful reconstructions of objects from a wide variety of reflectances including smooth, rough, diffuse and specular surfaces, even in the presence of significant attached shadows. Finally, we empirically prove that under these challenging settings we obtain more accurate shape reconstructions than existing methods. [ABSTRACT FROM AUTHOR]