| Biol 591 |
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Fall 2003
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Scenario
3: Comparison of protein sequence against database
How to run the DG47 DNA sequence through Blast
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| Go to http://www.ncbi.nlm.nih.gov/ | This is the National Center for Biological Information (NCBI) site, home of Blast and much else. Why not bookmark it? |
| Click on the Blast on the blue bar near the top | |
| Click in the Standard nucleotide-nucleotide BLAST [blastn] under Nucleotide BLAST | There many flavors of Blast, depending on what kind of sequence you have (DNA or protein) and what you want to compare it against (DNA or protein). The other choices under Nucleotide BLAST are for specialized purposes. |
| Paste the DG47 sequence into the Search box. If you don't have the sequence, get it now by clicking here | (If you're just now downloading the file, you're browser may ask you whether you want to save it or open it. You can open it in Notepad, but eventually, you need to save it, since we'll be using it later). It's best to copy the entire file into the Search box, including the FastA header (the line beginning >), because Blast recognizes the header and uses the line as a label. |
| Click the Blast button. | This will bring you to a new page. Check the Query= line near the top. It should read Query = PCR Product DG47 (190 letters). Note the time estimate below the Format button. |
| Click the Format button. | This will open up a new window, which will refresh itself until Blast is ready with the output.. |
| When the output arrives, scroll down to the box below Distribution of n Blast Hits... for results in graphical form and further down for results in text form. | We'll discuss significance in due course. For now, suffice to say you were expecting an E value of less than 10-30. A value close to 1 is pretty pitiful. |
| Congratulate self | You're done! |