Steps by step Using BLAST for STS

At first I have nucleotides sequence and I want to find STS on it. I choos BLAST (Basic Local Alignment Search Tool) from NCBI for search for STS on my nucleotides and copare or align with other submitted nucleoties. I do steps by step folowing below demonstration.

1. Prepare data as "FASTA" format (nucleotides sequence)…. I have single strand DNA, 1500 nucleotides long.

Find BLAST by internet searching tools….I fine in NCBI webpage http://www.ncbi.nlm.nih.gov/BLAST/

And then, select " Standard nucleotides-nucleotides BLAST or [blastn]

2. Now we are already to perform alignment by BLAST on this web based available tool.

3. Copy data and then past in box “Search” and fill in blank of “Set subsequence”

4. Choose database as dbSTSs.

5. You can fill in other option by pull down scrall bar and fill in blank….but I’ll not do it this time.

6. Click “BLAST” then get result.

7. Keep the request ID....In case of we want to submit dbSTSs.

8. You can change format….but again, I’ll not change anything.

9. Now I’ll check for my STS BLAST result…..click “Format”.

10. Then, get result of alignment for STSs...............................

11. In result, we’re now get score of alignment with nucleotides sequence from many species.

Briefly, the result show 39 BLAST sequences can be aligned with my sequence with diferrent score respectively. I'm now know BLAST score (2932) very high when do alignment compared with “Streptococcus mutans UA159” because I did copied this sequence to demonstrate to you.

.……..Yes, it’s Streptococcus mutans UA159. *-*

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In this BLAST tool, give us many in formations that we can learn from it much more. But I’ve to confess that I’m not good to show you in detail now. This is an idea I learn by myself in short period. I think we can do it better if we spend more time with it and improve skill should be done.

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