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General Research Use collection streamlines access to patient-level data in dbGaP
In response to many requests from dbGaP users to simplify and streamline the data access request process while respecting patient consent, dbGaP staff have identified “General Research Use” individuals from different studies and created a collection that allows users to access data on these individuals through a single access request.
Read more...NCBI Southern California Regional Workshops to be held June 30 - July 2
NCBI Service Desk staff will present a workshop series (June 30 - July 2, 2015) at the Beckman Research Institute of City of Hope in Duarte, California. These five individual modules include lectures and hands-on demonstrations intended for physicians and researchers who want to learn more about NCBI resources and how to use them to advance research projects.
New YouTube video: "Sequence Viewer: Navigate Objects with Jump Arrows"
The newest video on the NCBI YouTube channel, "Sequence Viewer: Navigate Objects with Jump Arrows", introduces jump arrows, a feature recently added to Sequence Viewer. A full list of new features, improvements and fixes can be found in the release notes.
UniVec build 9.0 now available for VecScreen searches and FTP
UniVec, NCBI's non-redundant database of vector sequences, has been updated to build 9.0, which enables searches run using NCBI's VecScreen tool to detect more of the foreign sequences introduced during the cloning or sequencing process. UniVec build 9.0 is also available via FTP.
BLAST+ stand-alone updated to version 2.2.31
A new version (2.2.31) of the stand-alone BLAST executables (Linux, Windows and MacOSX on FTP) is now available. New features include support for BLAST-XML2 specification (information here) and JSON BLAST output format, as well as several bug fixes and improvements. The BLAST AMI at AWS will also be updated to 2.2.31 (see this BLAST Help page for more information). For a full list of improvements, see the release notes.
Complete MERS coronavirus genomes from China and South Korea are in GenBank
Two complete MERS coronavirus genomes are in GenBank: one from China (KT006149) and one from South Korea (KT029139). In addition, the MERS coronavirus resource page gives users an easy way to find all sequences related to this pathogen.
dbSNP build 144 now available
dbSNP build 144 data is now available through the integrated NCBI Entrez system and FTP. This release includes data for human, chicken, soybean and horse. Build 144 provides more than 601 million submitted and 191 million reference variants for 4 species. To see complete build statistics, visit the SNP summary page.
NCBI Sequence Viewer version 3.8 available
NCBI Sequence Viewer has recently been updated and now has a new track navigation GUI that allows you to quickly find features like gene, exon, SNP and alignment; it also has a new API option for negative graph values and improved variation tooltips. A full list of new features, improvements and fixes is included in the release notes.
June 10th webinar: "Working with Phylogenetic Trees in Genome Workbench"
On June 10th, NCBI staff will show you how to use NCBI's powerful Genome Workbench application to work with phylogenetic trees. You will learn about the many options for importing trees, for visualizing, searching and modifying the trees and for saving or exporting them. We will also answer questions and welcome feedback from our participants on future directions for Genome Workbench.
Conserved Domain Database (CDD) version 3.14 now available online and via FTP
Conserved Domain Database (CDD) version 3.14 is now available with 560 new or updated NCBI-curated domains and 50,648 total domain models from CDD's database providers: Pfam, SMART, COG, TIGRFAMs, Protein Clusters, and the NCBI in-house curation project.
The SRA Submission App on BaseSpace lets you submit directly to SRA
If you use Illumina for next-gen sequencing and want or need to share your genomic data by putting it into a public repository, you can now submit directly to SRA through BaseSpace. You can also submit directly to SRA if you use Mothur for 16S assembly. Note: it is possible to port data from SRA into BaseSpace; click here for instructions.
New NCBI YouTube video: "NCBI Minute: Prokaryotic Genome Annotation Update"
The newest video on the NCBI YouTube channel describes the updates recently made to our prokaryotic genome annotation process. In addition to describing the improvements to RefSeq bacterial and archaeal genome annotation and management, we also provide tips on adapting your workflow and show you how to find more information and help.
New NCBI YouTube video: "Genome Workbench: Import BAMs and Export Alignments"
This video on the NCBI YouTube channel shows you how to import BAM files, create a BAM file index, and export selected alignments using NCBI's Genome Workbench.
June 3rd webinar: "Troubleshooting GenBank Submissions: Coding Region Annotation"
Next Wednesday, June 3rd, NCBI staff will show you how to troubleshoot internal stop codon errors encountered during coding region (CDS) annotation. The source of this problem can be in (1) improper frame/strand, or genetic code designation or (2) poor sequence quality. You will learn how to analyze your sequences and uncover problems with BLAST prior to submitting them to GenBank.
NCBI to hold three-day genomics hackathon in August
From August 3-5, NCBI will host its second genomics hackathon focusing on advancing bioinformatics analysis of next generation sequencing data. This event is for students, postdocs and investigators already engaged in the use of pipelines for genomic analyses from next generation sequencing data.* Working groups of 5-6 individuals will be formed for twelve teams, in three sections. These groups will build pipelines to analyze large datasets within a cloud infrastructure. The sections for this iteration are:"RNA-Seq Normalization for Every Biologist", "Translational Genomics", and "Democratization of Genomics". Please see the application for specific team projects.
New NCBI YouTube Video: NCBI's Tree Viewer
This short video, "NCBI's Tree Viewer" on the NCBI YouTube channel is an introduction to Tree Viewer, a tool for viewing your own phylogenetic tree data. Tree Viewer is customizable and can be embedded in a wide variety of web pages.
New NCBI Insights blog post: "NCBI's First Hackathon: Advanced Bioinformatic Analysis of Next-Gen Sequencing Data"
In the latest blog post on NCBI Insights, we discuss the genomics hackathon NCBI hosted earlier this year, in conjunction with the NIH Office of Data Science. The goal was to have experienced genomics professionals create efficient pipelines for people who are new to this field.
May 26th webinar: "The NCBI Minute: Prokaryotic Genome Annotation Update"
The next NCBI Minute on Tuesday, May 26th will cover recent improvements to the way we annotate and manage RefSeq bacterial and archaeal genomes at NCBI. We'll introduce you to the new annotation paradigm, provide tips on adapting your workflow, and point out how to find help and more information.
New NCBI Insights blog post: "NCBI RefSeq's Antimicrobial Peptide Indexed Field: Facilitating Novel Antibiotic Discovery"
The latest blog post on NCBI Insights introduces the RefSeq "Protein has antimicrobial activity [prop]" indexed field, which retrieves curated sequence annotations showing naturally occuring antimicrobial peptides (AMPs), making it easier for researchers to identify alternatives to traditional antibiotics.
Export data into Genome Workbench with Tree Viewer version 1.4
NCBI Tree Viewer 1.4 implements several new features, improvements and bug fixes, including an updated Download function, which now allows you to export data into Genome Workbench; you can also upload custom user-defined data in ASN.1 and Newick formats. To see the full list of updates, see the Tree Viewer release notes.