An examination of the genotyping error detection function of SIMWALK2

This investigation was undertaken to assess the sensitivity and specificity of the genotyping error detection function of the computer program SIMWALK2. We chose to examine chromosome 22, which had 7 microsatellite markers, from a single simulated replicate (330 pedigrees with a pattern of missing genotype data similar to the Framingham families). We created genotype errors at five overall frequencies (0.0, 0.025, 0.050, 0.075, and 0.100) and applied SIMWALK2 to each of these five data sets, respectively assuming that the total error rate (specified in the program), was at each of these same five levels. In this data set, up to an assumed error rate of 10%, only 50% of the Mendelian-consistent mistypings were found under any level of true errors. And since as many as 70% of the errors detected were false-positives, blanking suspect genotypes (at any error probability) will result in a reduction of statistical power due to the concomitant blanking of correctly typed alleles. This work supports the conclusion that allowing for genotyping errors within likelihood calculations during statistical analysis may be preferable to choosing an arbitrary cut-off

RSAT 2011: regulatory sequence analysis tools

RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/

Early Agriculture in the Maya Lowlands

Wetland research in northern Belize provides the earliest evidence for development of agriculture in the Maya Lowlands. Pollen data confirm the introduction of maize and manioc before 3000 B.C. Dramatic deforestation, beginning ca. 2500 B.C. and intensifying in wetland environments ca. 1500-1300 B.C., marks an expansion of agriculture, which occurred in the context of a mixed foraging economy. By 1000 B.C. a rise in groundwater levels led farmers to construct drainage ditches coeval with the emergence of Maya complex society ca. 1000-400 B.C. Field manipulations often involved minor modifications of natural hummocks. Canal systems are not as extensive in northern Belize as previously reported, nor is there evidence of artificially raised planting platforms. By the Classic period, wetland fields were flooded and mostly abandoned

Burning down the brewery: establishing and evacuating an ancient imperial colony at Cerro Baúl, Peru.

Abstract: Before the Inca reigned, two empires held sway over the central Andes from anno Domini 600 to 1000: the Wari empire to the north ruled much of Peru, and Tiwanaku to the south reigned in Bolivia. Face-to-face contact came when both colonized the Moquegua Valley sierra in southern Peru. The state-sponsored Wari incursion, described here, entailed large-scale agrarian reclamation to sustain the occupation of two hills and the adjacent high mesa of Cerro Baúl. Monumental buildings were erected atop the mesa to serve an embassy-like delegation of nobles and attendant personnel that endured for centuries. Final evacuation of the Baúl enclave was accompanied by elaborate ceremonies with brewing, drinking, feasting, vessel smashing, and building burning. andes | archaeology | empire | Inca | Per