BLink Help Document | Revised 05/06/2004 |
PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure |
Overview |
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Scope |
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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 |
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Display Options |
The header of a BLink display provides a number of options. Click on the option of interest below for more information about it. |
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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. |
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 |
Sort BLAST hits by taxonomy proximity |
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 |
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 |
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 |