A goal of sequence
alignments is to allow a researcher to determine whether two sequences show
enough similarity to infer that they are homologous to one another. With this
application, we will be able to perform pair-wise comparisons of a single
sequence with sequences in a database using programs such as BLAST, WU-BLAST,
or FASTA. We will be using WU-BLAST (Washington University – BLAST) because the
program is fast and it allows gaps in the sequence. Similar to retrieving an organism
name when one has its sequence.
Instructions:
1. Click on the box
under program and select the WU-blastn option for nucleotide sequence
alignment.
2. Select and copy (or type) your nucleotide sequence (or
Accession or GI identification 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 “RUN
BLAST” 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, please refer to the Help section of the program.
When you
are ready, click here to start.
WU-Blast2 at
the European Bioinformatics Institute (EBI)