Interested in integrating data from clinical genetic testing and the literature in a single place? ClinVar aggregates information from a variety of sources about sequence variation and its relationship to human health in a single centralized location. from Intro to ClinVar: The goal of ClinVar is to provide a freely accessible, public archive of reports [...]
Entries Tagged as 'NCBI'
NCBI’s ClinVar
November 9th, 2012 by Kristi · No Comments
Tags:2012, clinical, gene, genetic, informatics, NCBI, repository, sequence, variation
NCBI Discovery Workshop
November 6th, 2012 by Kristi · No Comments
Washington University School of Medicine participated as a remote site for the National Center for Biotechnology Information (NCBI) Discovery Workshop held at the University of Michigan in October 2012. The workshop focused on a variety of NCBI resources and consisted of the following four sessions: Sequences, Genomes and Maps Proteins, Domains and Structures NCBI BLAST [...]
Tags:2012, database, genome, genomics, Information, NCBI, software, tool, tutorial, Washington University, webinar
GEO2R tool from NCBI
April 25th, 2012 by Kristi · No Comments
From the site: Use GEO2R to compare two or more groups of samples in order to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. A new video on NCBI’s YouTube channel shows how to use GEO2R.
Tags:2012, expression, NCBI, software, tool
NCBI and IPv6
February 21st, 2012 by Kristi · No Comments
From NCBI: NCBI now supports IPv6 (beta) for data downloads at http://bit.ly/xiQAsj. More information at http://1.usa.gov/x655AL . Please note that NCBI will be taking part in the World IPv6 Launch (http://www.worldipv6launch.org/). On that day (currently anticipated as June 6, 2012), we plan to add IPv6 service to our main FTP Server (http://bit.ly/yerWAX) and shortly thereafter [...]
Tags:2012, bioinformatics, Information, NCBI, research, science
Tutorials and lecture materials from NCBI and NHGRI
November 30th, 2011 by Kristi · No Comments
I am constantly surprised by the amount of great instructional material available in topics related to genomics and bioinformatics. It is unfortunate that there isn’t a “master list” somewhere of all of the instructional available from NIH-related efforts (hint hint). Until that happens, I’ll try to share resources as I find them. Here are some [...]
Tags:bioinformatics, BLAST, course, data, database, education, genetic, genome, genomics, informatics, Information, NCBI, NHGRI, research, science, tool, tutorial
NCBI C++ Toolkit v7.0.0 available
June 28th, 2011 by Kristi · No Comments
From NCBI: The NCBI C++ Toolkit v7.0.0 is now available from the FTP site. The Toolkit contains C++ language sources of NCBI software that can be used to build standalone BLAST, Sequin, Cn3D, and other NCBI tools and utilities. Also check out the The NCBI C++ Toolkit Book, Edited by Denis Vakatov, on the NCBI [...]
Tags:2011, bioinformatics, BLAST, genomics, informatics, Information, NCBI, NIH, research, software
Lecture Announcement: Bioinformatics (data, databases, & software)
May 2nd, 2011 by Kristi · No Comments
I am really excited to close out the “Genomic Techniques and Analysis” section of the Introduction to Genomic Medicine lecture series today with an introduction to bioinformatics and suggestions of how you can apply tools and databases to research. I’ll cover a number of topics, including: some general concepts to keep in mind when searching/using/analyzing [...]
Tags:2011, bioinformatics, BLAST, data, database, event, genome browser, ICTS, informatics, Information, NCBI, research, St. Louis, tutorial, Washington University
Happy Anniversary, National Library of Medicine!
March 14th, 2011 by Kristi · No Comments
This year marks the 175th anniversary of the National Library of Medicine. NLM is an important part of our day – whatever would we do without PubMed and NCBI? Of course NLM offers many other services and resources in addition to PubMed and NCBI. Visit NLM at http://www.nlm.nih.gov to learn more. For details on NLM’s [...]
On human contamination in databases…
February 19th, 2011 by Kristi · No Comments
Longo MS, O’Neill MJ, O’Neill RJ, 2011 Abundant Human DNA Contamination Identified in Non-Primate Genome Databases. PLoS ONE 6(2): e16410. doi:10.1371/journal.pone.0016410 Abstract During routine screens of the NCBI databases using human repetitive elements we discovered an unlikely level of nucleotide identity across a broad range of phyla. To ascertain whether databases containing DNA sequences, genome [...]
dbVar — Database of Genomic Structural Variation
September 30th, 2010 by Kristi · No Comments
The folks at NCBI are at it again! They’ve recently launched the Database of Genomic Structural Variation or dbVar. dbVAR “contains information about large-scale genomic variation, including large insertions, deletions, translocations and inversions. dbVar also provides associations of defined variants with phenotype information” and will contribute to our understanding of how differences in DNA contribute [...]
