BLASTP EXERCISE

by Frank Deis


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.  We will be looking at proteins which means we will be using BLASTP (BLAST for Proteins).  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 will have to come back to the main page. 

 

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/) the top right box is labeled "Protein."  Click on "Search for short, nearly exact matches."  Near the top of the page is a large rectangular search box.  Type in your name, first (middle?) and last, remembering that the letters ZB, JOUX do not occur in protein sequences.  If your name is "JOB" use a nickname.  Click on the button that says "BLAST!"

 

3.         You will get a page that says "formatting BLAST."  Wait a few seconds (not an hour!) and then click the button that says "Format!"  The resulting page is a little confusing with lots of data on it.  First there is a graph, "Distribution of 100 Blast Hits on the Query Sequence."  You can ignore that for the moment, and scroll down the page until you get to "Sequences producing significant alignments."  The best alignments are at or near the top.  Clicking on the Score (a number to the right, like 29.3) takes you down to where you can see the alignment.  If you are looking for a certain species you should scan up and down the alignments to find that species.  Clicking on the accession number to the left (usually letters and numbers like NP_192253) will take you to a separate page devoted to that protein.  Scrolling to the bottom of that page will give you the complete sequence of that protein.

 

4.         For your name, find the best match and submit the accession number, the species, and the complete sequence with your name underlined or otherwise marked.  Submit this on SAKAI  Some student mail goes into my SPAM folder so if you don't have an eden account, you should also hand it in on paper.  Note that the best aesthetic match is not always the sequence at the top of the list. But the top match on the list is always an acceptable answer. You are NOT likely to find your whole name. I was lucky.

 

MY ANSWER WOULD BE FROM photobacterium profundum

 

CAG22280.1  putative methyl-accepting chemota...  24.4 

 

ORIGIN      

  1 mfnmtlrqkl alsasiaiii ggllvtafsf lsslgrldsd inkqlngtas synnyvsnwl

 61 dskgtvlsam pvnisqdtle lhlqqvrdsa gfdnvflafs dgtqanannv ilppgnndpr

121 qwhwyqnain lngkvtvenp tvaaatgasv vsmgkavsif gqqavlgadv emsdiikqld

181 dvvlpgegym fiandkgnif ahadtsllnk svnakdrdlt dsmlkrlare ghvekenitg

241 nesyvfvkpi qgtnlstviv idynsvaapl ysslyeqifm tllvvvicaf lfnlfcvylf

301 kplqqvskal aviaqgggdl tqrinidsnd evgdlarnfn qftaslqvli ghirsqgvel

361 sqasaesefr anksadelnr qqdeismvat avtemasatq eiashaeqta raaqdstdht

421 nsgrelvvqs rvsinnlaee vnqatsvise lnehaqnins ilstiqgiae qtnllalnaa

481 ieaarageqg rgfavvadev rvlsqrthts teeiqsmiat lqqttskavg lmetssqlaq

541 csvddadqat valeqindsv alisdmatqi ataaeeqthv tseitlnttt ikdvtdqlve

601 daiaarhqae alsiqatkln dkvstfvv//