CHGV (Duke University) Ensembl Genome Browser PLINK This page describes some basic file formats, convenience functions and analysis options for rare copy number variant (CNV) data. Support for common copy number polymorphisms (CNPs) is described here. Copy number variants are represented as segments. Basic support for segmental CNV data The basic command for reading a list of segmental CN variants is plink --cnv-list mydata.cnv --fam mydata.fam --map mydata.cnv.map which can be abbreviated plink --cfile mydata (note that the map file must have the .cnv.map map extension). FID Family ID IID Individual ID CHR Chromosome BP1 Start position (base-pair) BP2 End position (base-pair) TYPE Type of variant, e.g. 0,1 or 3,4 copies SCORE Confidence score associated with variant SITES Number of probes in the variant Having a header row is optional; if the first line starts with FID it will be ignored. The FAM file format is the first 6 fields of a PED file, described here; this file lists the sex, phenotype and founder status of each individual. and then
Protein Data Bank - RCSB PDB A Structural View of Biology This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond. Use this website to access curated and integrated biological macromolecular information in the context of function, biological processes, evolution, pathways, and disease states. A Molecular View of HIV Therapy January Molecule of the Month Nuclear Pore Complex Deposition Preparation Tools Data Extraction Small Molecules Ligand Expo: Search the Chemical Component Dictionary for the IDs of released ligands Data Format Conversion 3D Structure Viewers
ASHG 2010: 1000 Genomes Project Tutorials ASHG 2010: 1000 Genomes Project Tutorial Videos The 1000 Genomes Project has released the data sets for the pilot projects and for more than 1000 samples for the full-scale project. A tutorial for how to use the data was held at the 2010 American Society of Human Genetics (ASHG) annual convention on November 3. Videos for each of the tutorial sessions are now available. All PowerPoints listed below are in PDF format. 1000 Genomes Project Tutorial Videos and Powerpoint Slides Top of page PennCNV PennCNV: copy number variation detection Welcome! PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. Click the menu to the left to navigate through the PennCNV website. What’s new: : Updated PennCNV version (June 2011) can be accessed in the Download page. : User-contributed programs (December 1 , 2010 and Feburary 27, 2011) to convert PennCNV call to PLINK format, and to plot PennCNV rawcnv file on multiple individuals to a high solution PNG file for comparing CNV calls across individuals. : Minor changes to visualize_cnv.pl in the Download page (August 09 , 2010) to improve graphics (JPG/PDF) production and immitate Illumina GenomeStudio screen shots. : A few minor changes to helper scripts can be accessed in the Download page (June 07, 2010). Reference:
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