BLink Help Document Revised 05/06/2004
PubMed Entrez BLAST OMIM Taxonomy Structure

  1. Overview
  2. Display Options
  3. Additional Options

Overview back to top

Scope back to top

BLink ("BLAST Link") displays the results of BLAST searches that have been done for every protein sequence in the Entrez Proteins data domain.

To access it, follow the BLink link displayed beside any hit in the results of an Entrez Proteins search.

In contrast to Entrez's "Related Sequences" feature, which lists the titles of similar sequences, BLink displays the graphical output of pre-computed blastp results against the protein non-redundant (nr) database. The output includes the positions of up to 200 BLAST hits on the query sequence, scores, and alignments. (View sample BLink output for human MLH1 protein.)

BLink offers a variety of display options, including the distribution of hits by taxonomic grouping, the best hit to each organism, the protein domains in the query sequence, similar sequences that have known 3-D structures, and more.

Additional options allow you to specify which taxa you would like to exclude, increase or decrease the BLAST cutoff score, or filter the BLAST hits to show only those from a specific source database, such as RefSeq or Swiss-Prot.   Click on a display option below for additional information about it.

Sample Questions that can be answered with BLink back to top

  1. What protein sequences are similar to an Entrez protein sequence of interest, and what is the position and BLAST score of each hit? (see All Hits)

  2. What are all the organisms to which the sequence gets hits? Display the best hit to each organism? (see Best Hits)

  3. Display all the hits from organism X. (see Best Hits)

  4. What is the taxonomy tree structure of the organisms to which I got hits? Remove the hits from taxon Y. (see Common Tree)

  5. What are the most closely and distantly related organisms to which my sequence gets hits? (see Sort by Taxonomy Proximity)

  6. What protein sequences with known 3-D structures are similar to the query sequence? (see 3D Structures)

  7. What domains are present in the query sequence? (see CDD Search)

  8. How can I display and save the BLAST hits in FASTA format? (see GI List)

Display Options back to top

The header of a BLink display provides a number of options. Click on the option of interest below for more information about it.
   66 BLAST hits to 19 unique species Sort by Taxonomy Proximity
Keep only

Displays up to 200 similar protein sequences that were found by a blastp search against the protein non-redundant (nr) database, using the default BLAST parameters. The BLAST hits are sorted by score. Clicking on the score of any hit displays a pairwise alignment between the hit and the query sequence, based on BLAST 2 Sequences. Clicking on the GI number of any hit displays a BLink report which uses that sequence as the query.

Displays the top hit to each organism represented in the BLAST results. The Best Hits display also shows the number of hits to each organism. Click on the number to see only the hits to that organism.

Shows the position of the organisms, to which BLAST hits were found, in the taxonomic tree. If desired, taxa can be deleted in this display. Pressing the "Go Back" button then returns to the graphical display of BLAST results; however, sequences from the taxa you deleted are no longer shown.

Links to the Taxonomy BLAST (TaxBLAST) report available through NCBI's BLAST pages. Displays (1) an organism report, which sorts the BLAST hits according to species, (2) a lineage report, which gives a simplified view of the relationships between the organisms, according to their classification in the taxonomy database, and (3) a taxonomy report, which shows more detail about the relationships among all of the organisms found in the BLAST hit list.

Shows only the hits to protein sequences that are associated with known 3-D structures from the Molecular Modeling Database (MMDB). Clicking on the blue ball for any hit will open a new page that allows you to launch the Cn3D structure viewer (press the "View Structure" button). Cn3D will then display the structure as well as the alignment between the query sequence and the structure's protein sequence. Note that the Cn3D viewer must be installed on your computer, and set up as a helper application to your browser, in order to view the 3-dimensional protein structure.

Shows the domains in the query protein sequence, based on a comparison of that sequence to the Conserved Domain Database (CDD). A brief description of CDD is available on the NCBI Site Map. The CDD Help document provides detailed information.

Displays the titles of the BLAST hits being shown in the current display. The titles are displayed in Entrez Proteins, which in turn allows you to save the records in the desired format. For example, sequences can be saved in FASTA format for use in analytical software, such as a multiple sequence alignment program.

Additional Options back to top

Sort BLAST hits by taxonomy proximity back to top

The option to "Sort by Taxonomy Proximity" displays BLAST hits according to the taxonomic tree, starting with organisms most closely related to the source organism of the query sequence. Within a species, the BLAST hits are sorted by score.

Filter BLAST hits by major taxonomic groups back to top

BLink allows you to display or exclude BLAST hits from the major taxonomic groups shown above.

Clicking on the name of a taxon excludes all organisms from that taxon from the BLAST results display.  Clicking on the name again brings those hits back into the display.  In the example above, Bacteria and Fungi have been excluded.

The box to the left of each taxon shows the number of hits to that taxonomic group.  Clicking on the box displays all the hits from that group.

Filter BLAST hits by source database or BLAST cutoff score back to top

Keep only

The pop-up menu beside the "Keep Only" option allows you to display the BLAST hits from a source database of interest. For example, you can choose to display only the hits to RefSeq records, or only those sequences which are members of COGs. To see the choices, open the pop-up menu above.

The cutoff option allows you to specify a BLAST cutoff score that is higher or lower than the default of 100.

Questions or Comments?
Write to the NCBI Service Desk