Retiring and replacing the BLink protein similarity service


NCBI is discontinuing the BLink protein similarity service effective immediately. BLink provided graphical access to related proteins from protein records in the Entrez system. Because of the increasing volume of data in the protein database, BLink has become less useful as a tool for finding related sequences and is no longer maintainable.

Temporary replacement for BLink

The BLink service will redirect to a live protein-protein BLAST search against the Landmark database used by SmartBLAST. The Landmark database, described in the SmartBLAST documentation , provides matches from 27 selected cellular organisms with well-annotated complete genomes representing a broad taxonomic range. The results from the redirected BLink search will be shown as a Tax BLAST report  as shown in the figure below. The Tax BLAST report emphasizes the taxonomic source of the protein matches as did the BLink output.  From this new starting point, you can explore additional protein similarities through the BLAST service by re-submitting the search against other blast databases including the non-redundant (nr) database.

A Tax BLAST report

Figure 1. The Tax BLAST report for proton ATPase A. (click to enlarge)

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SmartBLAST updated to provide more information, database matches


The SmartBLAST service has recently been updated to emphasize matches to the landmark database, which comprises the proteomes from 26 well-curated genomic assemblies. The display also now presents more information about conserved domains and details about the query.

SmartBLAST quickly finds the closest relatives to a protein query and evaluates the phylogenetic relationship among the query and matched sequences. You can start a SmartBLAST search from the SmartBLAST page or the BLAST home page. Read more about SmartBLAST on NCBI Insights.

Fast Sequence Inspection with ORFfinder + SmartBLAST


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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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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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Introducing PubMed Labs


Welcome to PubMed Labs!

PubMed Labs is all about you. It’s a new NCBI initiative for creating innovative and relevant products by involving you, our user community, from the beginning.

PubMed Labs is about experimentation. It’s a place where you’ll find early versions of new tools, experimental content, and proposed features, as well as an opportunity to suggest ideas to us.

PubMed Labs is about learning. It’s a place where the focus is on figuring out what works, where failure is OK because it’s a learning experience, and where any idea is welcome that can improve our services for our users.

PubMed Labs is about conversation. It’s a place where we can share future plans with you, and you can tell us how we’re doing. It’s a place where we all can come together to create resources that will benefit the broader scientific community.

Join the conversation!

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