NCBI (National Center for Biological Information) supports many versions of BLAST, including the comparision of two sequences that you supply. Here's how to do this.
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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 | (But be sure to browse the other facilities when you have a chance) |
| Scroll down to Pairwise BLAST and click in the BLAST 2 Sequences | This version of BLAST allows you to choose the flavor of blast and the sequences that will be compared. You could also do this on your own computer, if you've downloaded BLAST. |
| Click in the down arrow next to the Program window and choose the appropriate program. | 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). Choose BlastN for DNA-DNA comparisons. Choose BlastP for protein-protein comparisons. Click on Program for a description of other programs. |
| Paste a sequence into the first window supplied for that purpose; or click Browse to look for the sequence on your computer; or enter a GI identifier (from the GenBank file). | You can copy raw sequence or the sequence in FastA format (one comment line preceded by ">" followed by raw sequence). BLAST will use the FastA header in the output to identify your sequence. This particular implementation of BLAST ignores blanks and numbers embedded in the sequence. |
| Similarly, input a sequence into the second window. | |
| Click the Align button. | It's at the bottom of the page. |
| Congratulate self | You're done! |