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The HuRef Browser: a web resource for individual human genomics

Nelson Axelrod, Yuan Lin, Pauline C. Ng, Timothy B. Stockwell, Jonathan Crabtree, Jiaqi Huang, Ewen Kirkness, Robert L. Strausberg, Marvin E. Frazier, J. Craig Venter, Saul Kravitz, Samuel Levy
2008 Nucleic Acids Research  
The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef.  ...  The HuRef Browser is a unique and versatile tool for browsing genome assemblies and studying individual human sequence variation in a diploid context. The browser is available online at  ...  Lastly, we would like to thank Tom Emmel and Hank Wu for their support in administering the IT system resources.  ... 
doi:10.1093/nar/gkn939 pmid:19036787 pmcid:PMC2686481 fatcat:zevaguxaz5gefax4beu3gadggy

gEVAL - A web based browser for evaluating genome assemblies [article]

William Chow, Kim Brugger, Mario Caccamo, Ian Sealy, James Torrance, Kerstin Howe
2016 bioRxiv   pre-print
We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly  ...  For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly.  ...  Acknowledgements The authors would like to thank Richard Durbin for his support and helpful comments on the manuscript.  ... 
doi:10.1101/038638 fatcat:bhq5x5jwgbdovoax34vrf4soam

gEVAL — a web-based browser for evaluating genome assemblies

William Chow, Kim Brugger, Mario Caccamo, Ian Sealy, James Torrance, Kerstin Howe
2016 Bioinformatics  
We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly  ...  Motivation: For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly.  ...  Acknowledgement The authors would like to thank Richard Durbin for his support and helpful comments on the article. Funding This work was supported by Wellcome Trust grant 098051.  ... 
doi:10.1093/bioinformatics/btw159 pmid:27153597 pmcid:PMC4978925 fatcat:lrolp4phx5celhyvibnwi26dsy

The UCSC Genome Browser database: update 2011

P. A. Fujita, B. Rhead, A. S. Zweig, A. S. Hinrichs, D. Karolchik, M. S. Cline, M. Goldman, G. P. Barber, H. Clawson, A. Coelho, M. Diekhans, T. R. Dreszer (+15 others)
2010 Nucleic Acids Research  
Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome  ...  Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation  ...  The highlight of the year for the Genome Browser project was the release of a UCSC browser for the first new human genome assembly in 4 years.  ... 
doi:10.1093/nar/gkq963 pmid:20959295 pmcid:PMC3242726 fatcat:fnemefhmkbc65bmwbfxqlp7lpm

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

Kyongyong Jung, Jongsun Park, Jaeyoung Choi, Bongsoo Park, Seungill Kim, Kyohun Ahn, Jaehyuk Choi, Doil Choi, Seogchan Kang, Yong-Hwan Lee
2008 BMC Genomics  
Information for individual species can be quickly accessed via a new tool named the taxonomy browser.  ...  All data and functions are available at the web site  ...  Acknowledgements We thank Donghan Kim and Wonho Song for collecting genome sequences from various web sites.  ... 
doi:10.1186/1471-2164-9-586 pmid:19055845 pmcid:PMC2649115 fatcat:osncfeqrkzgiphtyvrj7zoj4hm

SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry

H. Xi, J. Park, G. Ding, Y.-H. Lee, Y. Li
2009 Nucleic Acids Research  
SysPIMP comprises of three layers: (i) a standardized data warehouse, (ii) a pipeline layer for maintaining human disease databases and X!Tandem and BLAST and (iii) a web-based interface.  ...  Based on this system, SysPIMP will be the platform for efficiently and intensively studying human diseases caused by mutation.  ...  ACKNOWLEDGEMENTS We are very grateful to Dr Chuan Wang for maintaining the database server. We also thank Kyongyong Jung for making the SysPIMP web site clean and clear.  ... 
doi:10.1093/nar/gkn848 pmid:19036792 pmcid:PMC2686442 fatcat:oxpghopzrzek5jdt2nwaawpo5y

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

Amol Shetty, Prashanth Athri, Kajari Mondal, Vanessa L Horner, Karyn Steinberg, Viren Patel, Tamara Caspary, David J Cutler, Michael E Zwick
2010 BMC Bioinformatics  
Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser.  ...  Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by  ...  Acknowledgements We would like to thank the Dr.  ... 
doi:10.1186/1471-2105-11-471 pmid:20854673 pmcid:PMC2955049 fatcat:xuc4m5facrbthid4ql3dt5ush4

CNVVdb: a database of copy number variations across vertebrate genomes

F.-C. Chen, Y.-Z. Chen, T.-J. Chuang
2009 Bioinformatics  
CNVVdb is a web interface for identification of putative copy number variations (CNVs) among 16 vertebrate species using the-same-species self-alignments and cross-species pairwise alignments.  ...  CNVVdb also provides information of pseudogenes and single nucleotide polymorphisms (SNPs) for the CNV-related genomic regions.  ...  ACKNOWLEDGEMENTS We thank the system manager of the UCSC Genome Browser for providing Chimpanzee, Macaque, Mouse, Rat, Chicken and Stickleback self-alignments.  ... 
doi:10.1093/bioinformatics/btp166 pmid:19321736 pmcid:PMC2682513 fatcat:c4ktg7uzhjclhnf3hscn57ofzy

Using population admixture to help complete maps of the human genome

Giulio Genovese, Robert E Handsaker, Heng Li, Nicolas Altemose, Amelia M Lindgren, Kimberly Chambert, Bogdan Pasaniuc, Alkes L Price, David Reich, Cynthia C Morton, Martin R Pollak, James G Wilson (+1 others)
2013 Nature Genetics  
Physical maps of the human genome, including the sequence of most of its euchromatic portions 1, 2 , are basic resources in human genetics and genomics research: they provide the framework for analysis  ...  Supplementary Material Refer to Web version on PubMed Central for supplementary material. Admixture mapping the human genome's missing pieces.  ... 
doi:10.1038/ng.2565 pmid:23435088 pmcid:PMC3683849 fatcat:qplnxrj7krbvblwqpmbl3ey4ke

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J. Enright, Ioannis Iliopoulos
2015 GigaScience  
We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer  ...  Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve.  ...  /Scribl/ Web-based The HuRef Browser [249] A web resource for individual human genomics http://huref.jcvi.org Web-based Table 5 5 Genome browsers (Continued) UCSC Cancer Genomics Browser [251  ... 
doi:10.1186/s13742-015-0077-2 pmid:26309733 pmcid:PMC4548842 fatcat:w7hxgunagfcbxctnio7kwnucsy

Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)

Sanjida H. Rangwala, Anatoliy Kuznetsov, Victor Ananiev, Andrea Asztalos, Evgeny Borodin, Vladislav Evgeniev, Victor Joukov, Vadim Lotov, Ravinder Pannu, Dmitry Rudnev, Andrew Shkeda, Eric M Weitz (+1 others)
2020 Genome Research  
NCBI's flagship genome browser, Genome Data Viewer (GDV), displays our in-house RefSeq annotation, is integrated with other NCBI resources such as Gene, dbGaP, and BLAST, and provides a platform for customized  ...  In addition, we report how users can add SV to their own web pages to create a custom graphical sequence display without the need for infrastructure investments or back-end deployments.  ...  Acknowledgments We thank Arkadi Doubintchik for aid in project management and the NCBI QA team and Marina Omelchenko for testing of our graphical viewers.  ... 
doi:10.1101/gr.266932.120 pmid:33239395 pmcid:PMC7849379 fatcat:mx7haygquja3xhrdp2vntshl3q

Mapping the Human Reference Genome's Missing Sequence by Three-Way Admixture in Latino Genomes

Giulio Genovese, Robert E. Handsaker, Heng Li, Eimear E. Kenny, Steven A. McCarroll
2013 American Journal of Human Genetics  
We used this approach to map the genomic locations of almost 20 megabases of sequence unlocalized or missing from the current human genome reference (NCBI Genome GRCh37)-a substantial fraction of the human  ...  A principal obstacle to completing maps and analyses of the human genome involves the genome's "inaccessible" regions: sequences (often euchromatic and containing genes) that are isolated from the rest  ...  Acknowledgments Web Resources The URLs for data presented herein are as follows: Figure 6 .  ... 
doi:10.1016/j.ajhg.2013.07.002 pmid:23932108 pmcid:PMC3971454 fatcat:q7wbon2cmbd3bfdsgngkexrzui

Nucleosome positioning: resources and tools online

Vladimir B. Teif
2015 Briefings in Bioinformatics  
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner.  ...  The purpose of this review is to cover a practical aspect of this field, namely to provide a guide to the multitude of nucleosome positioning resources available online.  ...  Three anonymous referees are acknowledged for interesting comments and encouragement to extend this work.  ... 
doi:10.1093/bib/bbv086 pmid:26411474 fatcat:entndwwjrndw3jdaf3raynfrj4

Linear assembly of a human centromere on the Y chromosome

Miten Jain, Hugh E Olsen, Daniel J Turner, David Stoddart, Kira V Bulazel, Benedict Paten, David Haussler, Huntington F Willard, Mark Akeson, Karen H Miga
2018 Nature Biotechnology  
As a result, human centromeric regions remain absent from even the most complete chromosome assemblies.  ...  Characterizing both the sequence composition of individual HOR structures and the extent of repeat variation is crucial to understanding kinetochore assembly and centromere identity 3-5 .  ...  , interquartile range) Clearly defined error bars See the web collection on statistics for biologists for further resources and guidance.  ... 
doi:10.1038/nbt.4109 pmid:29553574 fatcat:fhtuumjqlzb3ric23jzqhibtky

Very long haplotype tracts characterized at high resolution from HLA homozygous cell lines

Paul J. Norman, Steve J. Norberg, Neda Nemat-Gorgani, Thomas Royce, Jill A. Hollenbach, Melissa Shults Won, Lisbeth A. Guethlein, Kevin L. Gunderson, Mostafa Ronaghi, Peter Parham
2015 Immunogenetics  
The data we describe will provide a valuable resource for characterizing haplotypes, designing and refining imputation algorithms and developing assay controls.  ...  The HLA region of chromosome 6 contains the most polymorphic genes in humans.  ...  Acknowledgments We extend thanks to the members of the John Hansen laboratory at the Fred Hutchinson Cancer Research Center for supplying some of the (IHWG) cell line/DNA samples.  ... 
doi:10.1007/s00251-015-0857-y pmid:26198775 pmcid:PMC4540692 fatcat:tlxl25moinajvaptpk4tppac24
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