NCBI’s First Hackathon: Advanced Bioinformatic Analysis of Next-Gen Sequencing Data


This blog post is geared toward genomics professionals.

From January 5th-7th, 2015, NCBI, in conjunction with the NIH Office of Data Science, held a genomics hackathon, where genomics professionals gathered to write useful, efficient pipelines for people new to genomics.

After we announced the hackathon, over 130 qualified applicants expressed interest in attending. Four team leads chose 23 attendees from this pool, then assigned initial predefined roles and provided biological guidance for a product in one of four subject areas: DNA-Seq, RNA-Seq, Epigenomics and Metagenomics. Continue reading

NCBI RefSeq’s Antimicrobial Peptide Indexed Field: Facilitating Novel Antibiotic Discovery


This blog post is aimed toward biomedical researchers.

Antibiotic-resistant bacterial infections account for the deaths of tens of thousands of Americans every year. Over the past twenty years, these difficult to treat infections have become more common. Since traditional antibiotics are ineffective in these cases, biomedical researchers are looking for alternatives. NCBI’s RefSeq project has created a new indexed field, “Protein has antimicrobial activity [prop]“, to assist in this search by retrieving useful sequence annotation showing naturally occurring antimicrobial peptides, or AMPs.

Antimicrobial peptides are naturally occurring peptides from a diverse array of species that are a part of an organism’s innate immune system. The RefSeq team recently gathered a list of over 130 human genes encoding one or more experimentally proven AMPs. These peptides are typically less than 100 amino acids and can display bactericidal, antiviral, antifungal, and even antitumor activities, with a specific AMP usually having a subset of these activities. AMPs may be a suitable alternative to traditional antibiotics because they work quickly, efficiently, and tend to have broad spectrum activity. Moreover, since they are naturally-occurring, AMPs are less likely than other compounds to be toxic to host cells or to give rise to AMP-resistant bacterial strains. Continue reading

Accessing the Hidden Kingdom: Fungal ITS Reference Sequences


This post is geared toward fungi researchers as well as RefSeq and BLAST users.

Fungi have unique characteristics that can make it difficult to identify and classify species based on morphology. To address these issues, Conrad Schoch, NCBI’s fungi taxonomist, and Barbara Robbertse, NCBI’s fungi RefSeq curator, in collaboration with outside mycology experts, are curating a set of fungal sequences from internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA genes. This set of standard DNA sequences for fungal taxa not only addresses these difficulties in identifying and classifying fungal species by morphology, but is also essential for analyzing environmental (metagenomics) sequencing studies. The curated ITS sequences, described in a recent article in Database (PMC Free Article), all have associated specimen data and, when possible, are taken from sequences from type materials, ensuring correct species identification and tracking of name changes. This article will show you how to access these ITS sequences and search them using the specialized Targeted Loci BLAST service.

The fungal ITS sequences are a RefSeq Targeted Loci BioProject (PRJNA177353). As you may know, a BioProject is a collection of biological data related to a single initiative; in this case, the goal is to collect and curate fungal sequences from targeted loci – specific molecular markers such as protein coding or ribosomal RNA genes used for phylogenetic analysis.

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NIHMS Users: Do You Know How Often Your Paper is Being Accessed Via PMC? Here’s How to Find Out.


If you’re reading this, you probably already know that NIH and some other institutions have public access policies that require that peer-reviewed publications resulting from their funding be made available to the public. But did you know that if you complied with your funding agency’s public access policy by depositing your author manuscript in NIH’s PubMed Central (PMC) archive via the NIH Manuscript Submission (NIHMS) system, you can easily obtain statistics on how frequently your paper is being accessed? Continue reading

NCBI homepage update includes action buttons, category pages


The NCBI homepage now has six prominent buttons on it: Submit, Download, Learn, Develop, Analyze, and Research. Each of these buttons leads to an action page devoted to a particular set of services.

Figure 1. The NCBI homepage. The new action buttons are outlined in red.

Figure 1. The NCBI homepage. The new action buttons are outlined in red.

We’ve also included a blue feedback button on the left side of the Download, Learn, Develop and Analyze pages so that you can tell us what you think.

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Exploring Entrez Direct: Parsing the XML Output of E-utilities


Entrez Direct is a UNIX/LINUX command-line interface to E-utilities, the API to the NCBI Entrez system. One of Entrez Direct’s most useful features is its ability to parse and reformat complex XML data returns from EFetch. In this post, we will explore how to use these features to parse, reformat and process specific data from PubMed records downloaded in XML using EFetch. Though this post focuses on PubMed, the technique is universal and applies to any XML returned by E-utilities from any database. The example explored here is also presented briefly in the Entrez Direct documentation; here we’ll dive in a bit depeer to see how it works. Let’s get started!

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My Bibliography and SciENcv: How to Delegate Authority to Others to Edit/Create Your Profile and Collections


As a My NCBI account holder, you can invite other individuals to act as your delegate and grant them the ability to view and edit your My Bibliography collection (including Other Citations), as well as the ability to view, edit, and create profiles in your SciENcv.

Inviting a Delegate

The first step is to send a delegate invitation from your NCBI Account Settings page. After you’ve logged in to your NCBI account, click on your username in the top right corner of the screen to access your Account Settings. Then, under the “Delegates” section, click “Add a delegate” and enter the email address for your intended recipient. You can have multiple delegates on your account, and you can control what each delegate has access to from the Delegates section of your Account Settings page.

Acting as a Delegate

If a colleague invites you to become a delegate on their NCBI account, you will receive an email invitation. After you’ve accepted the delegation invitation, you will see your colleague’s Bibliography appear in your Collections list on your My NCBI landing page:

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NIHMS’s new look streamlines the manuscript submission process


Today, the NIH Manuscript Submission (NIHMS) system gets a new interface design, as well as updates that streamline the login and manuscript submission processes and provide relevant help information directly on each screen.

Homepage

NIHMS_New Homepage_Final

Figure 1. The new NIH Manuscript Submission system homepage.

The NIHMS sign-in routes will now be available from the homepage. Select a route based on your funding agency (1) or sign in through NCBI if you are starting a deposit on an author’s behalf (2).

The homepage also includes a graphic overview of the NIHMS process (3). You can hover over each step for more information or click “Learn More” to read the complete overview in the FAQ.

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Bald eagle and other bird genome sequence and annotation data publicly available at NCBI


A series of press releases, including one by Science Publishing, recently announced the first findings of the Avian Phylogenomics Consortium, who analyzed genome sequences and annotation data for 48 bird genomes representing all of the bird taxonomic orders. All of the sequenced genomes, along with any annotation provided by the submitter, are available in NCBI resources including Assembly, Nucleotide, Protein, the Sequence Read Archive (SRA), and BLAST, or from species-specific GenBank genomes FTP directories. RNA-Seq data for some of the bird species can be found in SRA.

With the exception of three very fragmented assemblies, NCBI annotated the genome assemblies submitted by the Avian Phylogenomics Consortium using NCBI’s Eukaryotic Genome Annotation Pipeline, and these annotations are now part of the RefSeq project. The RefSeq project also generated annotations for an additional 6 bird assemblies, for a total of 51 RefSeq genomes. A summary of all the bird genomes that have RefSeq annotation is here.

Figure 1. A selection of the bird genomes with RefSeq annotation. At the top right is a legend describing resource links for each bird genome. Detailed annotation reports, accessible through the "AR" link in the far right column, are available for those genomes annotated in 2014. RefSeq annotation is on organism-specific BLAST pages (the "B" link) and on FTP (the "F" link). Click on the picture to go to the summary table.

Figure 1. A selection of the bird genomes with RefSeq annotation. At the top right is a legend describing resource links for each bird genome. Detailed annotation reports, accessible through the “AR” link in the far right column, are available for those genomes annotated in 2014. RefSeq annotation is on organism-specific BLAST pages (the “B” link) and on FTP (the “F” link). Click on the picture to go to the summary table.

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Designing exon-specific primers for the human genome


A common task facing geneticists is to assay for sequence changes at particular locations in genes. These assays are often looking for changes in the coding exon of genes, and the target sequences are typically amplified using PCR from genomic DNA using a pair of specific primers. In this article, we will show you how to use NCBI Reference Sequences and Primer-BLAST, NCBI’s primer designer and specificity checker, to design a pair of primers that will amplify a single exon (exon 15) of the human breast cancer 1 (BRCA1) gene.

Here are the steps to follow to design primers to amplify exon 15 from human BRCA1:

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