Click on the image to see full-size! |
Point
your browser to www.ncbi.nih.gov. Click
on the “BLAST” button.
On the BLAST page, click on “BLASTP”, as shown in the thumbnail to the left. |
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Click on the image to see full-size! |
Previously, a file with the sequence of the HFE protein in FASTA format was saved to the desktop. Open this file, copy the FASTA file (including identifier, description line and sequence) and paste into the BLASTP search window as shown. |
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Click on the image to see full-size! |
The default setting is to search
for matches in all organisms. Often this is unnecessary, and only lengthens
the time to complete the search. A BLAST search can be made more efficient
by using the pull-down menu - as shown in the graphic to the left - to
limit alignments to a single taxon.
If the pull-down menu does not contain the limiting term which is desired, the scientific name, with the [ORGN] qualifier, can be typed into the "Limit by entrez Query" box (example: Canis familiaris [ORGN]).
In the “Options” box, limit the BLAST search by using the pull-down menu to select “Mammalia” (where you see "All organisms". This will limit the “hits” to only similar sequences which occur in Mammals. Leave the other options at their default values.
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Click on the image to see full-size! |
Click on the 
button below the Search boxes or at the bottom of the page to submit your
query. The screen shown in the graphic to the left should appear, which
indicates that the search has been submitted successfully to the BLAST
server at NCBI.
Although the search has been placed into a queue, it will only take approximately 8 seconds to search thousands of sequences and millions of amino acids! |
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A conserved
domain is a recurring sequence pattern or motif which occurs
within a larger sequence. A conserved
domain is associated with a characteristic structure and function,
and in concert with other domains, determines the function of the entire
protein.
Click on the |
button to open a new browser window that contains the BLAST results.
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Back to "Sequence similarity searching using NCBI BLAST" Back to "Index for ENTREZ and Data Base Searches" RETURN TO SITE MAP |