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The Genomedata format for storing large-scale functional genomics data

M. M. Hoffman, O. J. Buske, W. S. Noble
2010 Bioinformatics  
We present a format for efficient storage of multiple tracks of numeric data anchored to a genome.  ...  The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. We have also developed utilities to load data into this format.  ...  We introduce the Genomedata format for genome-scale numerical data, which uses an HDF5 (Hierarchical Data Format; http://hdfgroup. org/HDF5/) container for efficient, random access to huge genomic datasets  ... 
doi:10.1093/bioinformatics/btq164 pmid:20435580 pmcid:PMC2872006 fatcat:eazdsdvrmfhqxilq3jxkcw3dgm

Novel scripts for improved annotation and selection of variants from whole exome sequencing in cancer research

Marcus Celik Hansen, Line Nederby, Anne Roug, Palle Villesen, Eigil Kjeldsen, Charlotte Guldborg Nyvold, Peter Hokland
2015 MethodsX  
While obtaining data sets is a straightforward procedure, the subsequent analysis and interpretation of the data is a limiting step for clinical applications.  ...  •Extended annotation, relevance scoring and defining focus areas through the provided functions.  ...  Acknowledgements MethodsX thanks the reviewers of this article (Christos Noutsos and a second reviewer who would like to remain anonymous) for taking the time to provide valuable feedback.  ... 
doi:10.1016/j.mex.2015.03.003 pmid:26150983 pmcid:PMC4487347 fatcat:hrdqbnqw4jhk5itnptlbbwkuka

Identifying elemental genomic track types and representing them uniformly

Sveinung Gundersen, Matúš Kalaš, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Sandve
2011 BMC Bioinformatics  
The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that  ...  We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0.  ...  We thank Kai Trengereid for crucial work in developing the GTrack-related tools, and Inge Jonassen for valuable input on the BioXSD format.  ... 
doi:10.1186/1471-2105-12-494 pmid:22208806 pmcid:PMC3315820 fatcat:uq63xf6tzrf25jha7t2osog56m

The Global Relationship between Chromatin Physical Topology, Fractal Structure and Gene Expression

L. M. Almassalha, A. Tiwari, P. T. Ruhoff, Y. Stypula-Cyrus, L. Cherkezyan, H. Matsuda, M. A. Dela Cruz, J. E. Chandler, C. White, C. Maneval, H. Subramanian, I. Szleifer (+2 others)
2017 Scientific Reports  
The physical organization of the genome is regulated at a broad range length scales, extending from the primary folding structure of DNA around histones (< 10 nm) into micron scale hetero-and eu-chromatin  ...  Despite accessibility being largely influenced by the physical organization of the nuclear nanoarchitecture, most of what we know about key genomic processes, including transcription, comes from viewing  ...  Lawlor for his insight and comments regarding the results presented within the manuscript.  ... 
doi:10.1038/srep41061 pmid:28117353 pmcid:PMC5259786 fatcat:glf5gen4ljbpxet7puljud5iqu

Crustacean vitellogenin: a systematic and experimental analysis of their genes, genomes, mRNAs and proteins; and perspective to Next Generation Sequencing

Stephanie Jimenez-Gutierrez, Cristian E. Cadena-Caballero, Carlos Barrios-Hernandez, Raul Perez-Gonzalez, Francisco Martinez-Perez, Laura R. Jimenez-Gutierrez
2019 Crustaceana  
Those analyses confirm that the Vtg obtained from selected species will serve to understand the process of vitellogenesis in crustaceans that is important for fisheries and aquaculture.  ...  This work is a systematic analysis that compares the similarities and differences of Vtg genes, mRNA and Vtg between the crustacean species reported in databases with respect to that obtained from the  ...  We also thank the Advanced Computing and a Large Scale Group of the Industrial University of Santander (SC3-UIS), supported by the Vice-Rector for Investigation and Extension of the Industrial University  ... 
doi:10.1163/15685403-00003930 fatcat:zsowithi7bcrjn5icznjkxw2ry

Next-generation kinship, ancestry and phenotypic deduction for forensic and genealogical analysis

Margherita Colucci
This project explores the potential of genome-wide SNP chips and targeted massively parallel sequencing (MPS) in these areas.SNP chip data arguably forms the "gold standard" for kinship analysis.  ...  The three methods for dense autosomal SNP data performed comparably in kinship estimation and pedigree reconstruction. Kinship coefficients were estimated from the MPS data.  ...  We thank NUCLEUS Genomic Services at the University of Leicester for access to DNA sequencing.  ... 
doi:10.25392/ fatcat:5tyi653upzca7o6hsertpyw47u