Used to compare two
sequences with one another. Similar to multiple sequence alignment except that
we are not comparing to sequences in a database. Instead, we will be comparing
two sequences to each other for similarity. A good program for this application
is BLAST 2 Sequence developed by the National Center for Biotechnology
Information (NCBI).
Instructions:
1. Click on the box
under program and select the WU-blastn option for nucleotide sequence
alignment or blastp for protein sequence.
2. Select and copy (or type) your nucleotide sequence (or
accession or GI identifiction numbers) from
the FASTA format to empty box.
Select: Highlight your nucleotide sequence by clicking on the left mouse button, holding the button down while dragging the cursor over the region to be highlighted, then release mouse button.
Copy: Use command from the Edit box of the Explorer window or by pressing CTRL + C on the keyboard.
Paste: No specific format required. Use the Paste command from the Edit box of the Explorer window or press CTRL + V on the keyboard.
3. Click on the “Align”
button to start the program.
4. Program will list all
the sequences of the organisms closely related to your sequence.
The most similar will be at the top of the list and the less similar sequences will follow.
If you need more
assistance, click on the “Help” hyperlink in the WU-Blast program.
When you are ready, click
here to start.