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.
Ultimate replacement service for BLink
We would like to provide a more sophisticated replacement for BLink. Please provide comments on this post and let us know what features would be useful to you in a service that would allow you to quickly identify and sort related proteins. For instance:
- Are you interested in similar proteins in closely related or distantly related species or both?
- Are BLAST statistics important on the output?
- Is the ability to sort hits by taxonomy useful to you?
- Are there other sorting options that would be useful to you?
- What NCBI resources you would like to see linked to the protein similarity output (Gene, a genome browser, expression data, etc.)?
- Is the initial selection of species in the Landmark database a good starting set? Are there representative species you think should be added?
And if you are a previous user of BLink please let us know:
- What features of the BLink output did you find most useful?
- What features of BLink output that you found useful are missing in the Tax BLAST report?
- What advantages did BLink have for you over running a live blastp search with a protein of interest?
And, of course, provide any other suggestions here or via email to help us make a new protein similarity service that would be most useful to you.