Bottlenose dolphin annotation release 101


Annotation Release 101 for the bottlenose dolphin (Tursiops truncatus) is out in RefSeq! This annotation was based on the NIST Tur_tru v1 assembly, which has a four-fold increase in contiguity from the assembly used in the previous annotation. Over four billion RNA-Seq reads from skin and blood tissue were used for gene prediction. As a result of these improvements, the percent of partially-represented protein-coding genes went down from 24% to 4%. Over 2500 genes that were fragmented in the previous assembly were merged into complete genes. A total of 24,026 genes were annotated, and 17,096 of them were protein-coding. A full report on the annotation can be found here.

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Introducing Magic-BLAST


Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Magic-BLAST executables for LINUX, MacOSX, and Windows as well as the source files are available on the FTP site.

Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-Seq, locating the candidate introns and adding up the score of all exons. Sequencing reads can be provided as NCBI SRA accessions, FASTA or SRA files.

Magic-BLAST implements ideas developed in the NCBI Magic pipeline using the NCBI BLAST libraries. Magic-BLAST is under active development, and we expect the next few releases to occur on a monthly basis. Read more about Magic BLAST on the FTP site.

Fast Sequence Inspection with ORFfinder + SmartBLAST


intro pic

This blog post is intended for all BLAST users.

ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

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Troubleshooting GenBank Submissions: Annotating the Coding Region (CDS)


This article is intended for GenBank data submitters with a basic knowledge of BLAST who submit sequence data from protein-coding genes.

One of the most common problems when submitting DNA or RNA sequence data from protein-coding genes to GenBank is failing to add information about the coding region (often abbreviated as CDS) or incorrectly defining the CDS. Incomplete or incorrect CDS information will prevent you from having accession numbers assigned to your submission data set, but there is a procedure that will help you troubleshoot any problems with the CDS feature annotation: doing a BLAST analysis with your sequences before you submit your data.

Here’s how to use nucleotide BLAST (blastn) and the formatting options menu to analyze, interpret and troubleshoot your submissions:

1. To start the BLAST analysis, go to the BLAST homepage and select “nucleotide blast”.

nucleotide blast link. click to start BLAST analysis

Figure 1. Select “nucleotide blast”.

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SmartBLAST: Faster BLASTp search results in a graphical view


BLAST (Basic Local Alignment Search Tool) is a popular tool for finding sequences in a given database that are similar to a query sequence. Traditionally, BLAST displays these results as a sorted list of matches between the query and each database sequence. While this display is useful for examining how each subject sequence matches the query, it treats all subject sequences the same, regardless of the quality of the sequence data or its annotation, and also does not allow easy comparisons between different subject sequences.

For example, the subject sequences may fall into multiple groups of similar sequences, or all of the subject sequences may be more similar to each other than to the query. A common way to obtain this information is to construct a multiple sequence alignment of the query and some or all of the subject sequences, but to this point, BLAST has not provided such alignments directly.

Enter SmartBLAST! SmartBLAST is a new and experimental NCBI tool that makes it easier to complete common sequence analysis tasks, such as finding a candidate protein name for a sequence, locating regions of high sequence conservation, or identifying regions covered by database sequences but missing from the query.

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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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The Second Offering of “A Librarian’s Guide to NCBI” at NIH


NCBI, in collaboration with NLM and the National Network of Libraries of Medicine NLM Training Center (NTC) at the University of Utah, recently presented the second offering of A Librarian’s Guide to NCBI. Health Sciences Librarians from 17 universities and two federal agencies attended the five-day intensive course on the NIH campus. This second offering of the training continues to prepare health science librarians for supporting NCBI molecular databases and tools, and training patrons in the use of NCBI resources at their own institutions.

Participants and instructors from the 2014 “A Librarian’s Guide to NCBI” outside the National Library of Medicine.

Participants and instructors from the 2014 “A Librarian’s Guide to NCBI” outside of the National Library of Medicine.

As before, all the course materials are available online. Feel free to learn from them, adapt them for your own teaching, and share them with others. You can use the links below to access the updated 2014 course materials. These include the slide sets with demonstrations and practice problems.

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Making Custom Databases for Web BLAST


An easy way to speed up your BLAST analysis is to search a smaller database targeted to sequences of interest. We’ll describe here a few ways to create such custom databases on the BLAST web pages.  For this Quick Tip we’ll use the pages in the Basic BLAST section of the BLAST home page.

BLAST parent databases

Generating a custom database begins with selecting the appropriate parent database. The BLAST Guide provides database descriptions to help with choosing a database.  You select the parent in the Database pull-down menu, shown in Figure 1. Selecting the database is really your first opportunity to customize.

BLAST Parent Database Pull-down Menu

Figure 1. The database selection pull-down lists: top panel, nucleotide databases; bottom panel, protein databases

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New Pandoravirus Sequences are Accessible in GenBank


In the July 19, 2013 issue of the journal Science, an interesting article describes the discovery and characterization of two “giant” viruses that are proposed to comprise the first members of the “Pandoravirus” genus.

Nadege Philippe and co-workers obtained the viruses from sediment samples in Chile and Australia and found that they have no morphological resemblance to any previously defined virus families. The investigators isolated the genomes of these viruses and sequenced them using a variety of NextGen methodologies. They then assembled the reads into contigs and characterized them using various sequence similarity algorithms (including NCBI’s BLAST and CD-Search). Interestingly, while related to each other, the genomes were not similar to those of any other organism or virus. Additionally, 93% of protein-coding sequences had no recognizable homologs.

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Blastdbinfo: API access to a database of BLAST databases


NCBI offers extensive collections of sequences through its BLAST services (http://blast.ncbi.nlm.nih.gov) for comparing and identifying DNA, RNA and protein sequences. NCBI now deposits descriptions of these sequence collections, known as BLAST databases, in a special database called blastdbinfo that you can access through the Entrez Programming Utilities (E-Utilities). Using blastdbinfo, you can enable a program to find an appropriate database and then send BLAST searches to that database using either the BLAST URL API or standalone BLAST (installed locally).

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