Science Buddies: "Ask an Expert"

I have a project where I need to theorize the protein sequence of quail myoglobin. A very similar organism (chicken) has already had its myoglobin sequenced. I can access the entire genome of quail online. I can also access the gene nucleotide sequence and amino acid sequence of chicken myoglobin online as well.

I've been trying to use the tools on BLAST online to try and find similar sequences to the chicken myoglobin in quail but I am having significant difficulties. Could someone point me in the correct direction or walk me through how someone might do this? I think I was able to do it once but I forgot the steps.

I'm sorry it took so long to get a reply, but if you still need help, I'll do my best.

It's not clear to me whether you are having a specific problem with the results you are getting or if you aren't able to even do the search you want, so I'll talk you through the search part, and if you have problems after that, or if there is a specific problem you are having, just post again here, and I'll try to get back to you more promptly.

Start by going to this website:
http://blast.ncbi.nlm.nih.gov/Blast.cgi ... =BlastHome
Scroll down to Basic BLAST and select how you want to match. You can choose to use your nucleotide sequence of chicken myoglobin to search for a similar nucleotide sequence in the quail (in which case you would choose nucleotide blast) or you could use the protein (amino acid) sequence of chicken myoglobin to search for a known protein in the quail (choose protein blast). If you don't think the quail myoglobin is known, then I would recommend doing the nucleotide blast, but you can always do both (and play with some of the other options as well) and see how the outcome changes.

For your "query sequence", you would paste the gene sequence for chicken myoglobin (or the amino acid sequence if you chose to do protein). You can leave everything else in the top half of the screen blank (no need for a job title, query subrange, etc.) Below, where it says "Organism" type in either quail, or the scientific name for quail and select the organism from the list that will appear. Then, hit BLAST and let it search. It may take a minute or two since it is comparing to an entire genome. Once you get your results, you'll have to consider and analyze them. You'll likely have multiple areas of sequence similarity, many of which may have already been identified as specific genes/proteins.

I hope this helps, and again, if you run into any problems, please post again here and I'll try to help.
JMP