BLASTP: Step By Step


This is an exercise to show you how to use BLAST, which stands for "Basic Local Alignment Search Tool." To do an alignment, you have to have two sequences. BLAST is like Google for genes (it looks at DNA) and BLASTP is like Google for proteins (looking at amino acids). Here is a preliminary exercise:

  1. Go to http://www.ncbi.nlm.nih.gov. While you are there, make it a "favorite" or "bookmark" on your browser, since you might need to come back later.

  2. On the dark blue bar across the top of the page, click on BLAST. on the new page (http://www.ncbi.nlm.nih.gov/BLAST/) look at the headers, and find "Basic BLAST". The first two items under that header are "nucleotide blast" which you don't want, and "protein blast" which you do want. Click on that.

  3. The important part of the next page is the large box at the top that says "Enter Query Sequence". Type in your name (or your nickname, or your sister's name) remembering that the letters ZBJOUX are not recognized as amino acids. Ideally you should use your first and last name where possible. As you type in your name, the box turns yellow.

  4. Click on the large button below that says BLAST. Then wait. The rest of the process is automatic. First you get a message saying "Your search parameters were adjusted to search for a short input sequence". Continue to wait.

  5. Finally you will get a long list of hits. In my case the screen says "Distribution of 102 Blast Hits on the Query Sequence". Scroll down the page. There is no good reason not to use the highest scoring sequence. But remember that in this instance BLOSUM62 substitutions are working against you, in finding an exact match for your name. So just out of vanity you will probably want to scroll through the sequences and see what looks best. Scroll far down to the header that says "Alignments" and look to see which hits really resemble the name you entered. When you find one you like, click on the accession number, and scroll through to find the sequence.

  6. Please click through these images, noting that these are NOT LIVE WEB PAGES but .JPG images to help you understand the steps involved. Use your back arrow to return to this page after viewing:
    1. NCBI
    2. BLAST
    3. BLASTP
    4. BLASTP with sequence
    5. Right after BLAST button is clicked
    6. Later, results
    7. Highest ranked result
    8. Most aesthetic result
  7. DO NOT Send your results either on paper or by email. Instead as of 2012, submit only on SAKAI!

  8. MY PARTIAL ANSWER (you should submit entire sequence, with accession number and name of protein and name of organism) WOULD BE FROM photobacterium profundum

     

    ZP_01221459.1  putative methyl-accepting chemotaxis protein...  24.4 

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