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CHGV (Duke University) genome browser 72: Homo sapiens - Description Human Login/Register More ▼ Search Human Search all species Search Ensembl genomes Search Vega Search EMBL-EBI Search Sanger Favourite species All species Recent locations Clear history Recent jobs Human Homo sapiens What's New in Human release 83 More news... View karyotype Example region Genome assembly: GRCh38.p5 (GCA_000001405.20) More information and statistics Download DNA sequence (FASTA) Convert your data to GRCh38 coordinates Display your data in Ensembl Other assemblies Example gene Example transcript Gene annotation What can I find? More about this genebuild, including RNASeq gene expression models Download genes, cDNAs, ncRNA, proteins (FASTA) Update your old Ensembl IDs Additional manual annotation can be found in Vega Example gene tree Comparative genomics What can I find? More about comparative analysis Download alignments (EMF) Example variant Example phenotype Example structural variant Variation What can I find? More about variation in Ensembl Download all variants (GVF) Variant Effect Predictor Regulation Blog

Ensembl Genome Browser PLOS Genetics: A Peer-Reviewed Open-Access Journal 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

The Human Protein Atlas 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

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