CHGV (Duke University) Ensembl Genome Browser Data | 1000 Genomes Sample lists and sequencing progress A summary of sequencing done for each of the three pilot projects is available here. The list of samples and allocations is provided in a spreadsheet. Variant Calls Our variant calls are always released in vcf format. The released can be found in the release directory EBI|NCBI. Alignments The main project alignments are available in BAM format. Raw sequence files The main project raw sequence data is available in fastq format. Download data The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via our mirrored ftp sites. EBI FTP: NCBI FTP: Users in the Americas should use the NCBI ftp site and users in Europe and the rest of the world should use the EBI ftp site The data is also available via an Aspera server from both sites. An example command line for ascp looks like: FTP Hierachy The data dir The technical dir
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
User Page - sbgn.org SBGN study guide Visit the Documents section for: various examples (to get a better idea of what an actual map looks like) some tutorials (very accessible, but not always up-to-date) publications about SBGN (a good start for a brief historical overview) detailed technical specifications (the ultimate reference documents, most up-to-date, but a steep learning curve for beginners) some Frequently Asked Questions Please also check the SBGN PD User Manual when you are ready to draw your own maps. Quick overview The Systems Biology Graphical Notation comprises three complementary languages suited to represent different types of pathways. Process Descriptions (PD) is a language that permits the description of the processes (e.g. biochemical reactions) taking place in a biological system. Entity Relationships (ER) is a language that permits the description of all the relations involving the entities of a biological system. Language reference cards SBGN Bricks dictionary Getting started User Manual
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 National Center for Biotechnology Information