Science Buddies: "Ask an Expert"

Hi,

Would it be suitable to use partial protein sequences from the NCBI database and run BLAST to determine how similar species among a genus are? Are partial sequences reliable? If not, what are they used for? Furthermore, would it be possible to use partial sequences to see if somehow the similarities impact variation?

Thanks!

Hi,

Welcome to Scibuddies! We will try to help you do the most interesting and meaningful science project possible.

Sure, you can do a BLAST with just part of a protein but the problem is in choosing which part of the amino acid sequence to search with. Different parts of a protein do different things. Some amino acid sequences encode the catalytic part if the protein is an enzyme, some sequences contain regulatory elements like phosphorylation sites or cofactor binding sites. Some parts are necessary for dimerization. So, in order to do your BLAST with a partial protein sequence, the domain structure of the protein needs to be known. You might want to choose the domain that is critical for a particular protein's function because that is the one where mutations or polymorphisms would have the greatest effect. Some structural regions can show a lot of similarity to other proteins without them being much related in function.

Which proteins did you have in mind to compare and in which data base? Is this part of a science project? What is the question that you are trying to answer? The more information you give us about what you are planning, the better we can advise you.

Sybee

Thanks for posting a reply so quickly!

My research question is to find out what genomic similarities are present throughout the Falco genus. Specifically, I am hoping to use Falco femoralis, Falco peregrinus , and Falco cherrug. Among this genus, the peregrine falcon is no longer endangered, but it once was, and it's genome is available on the NCBI database; the saker falcon (Falco Cherrug) is endangered, and it's genome is available on the NCBI database; and Aplomado falcon (Falco femoralis) is endangered, but there are only partial protein sequences on the NCBI protein database.

I hope that by doing this, I can find out which genes are actually considered "superior" and contribute to evolution. In other words, if I can find that a certain gene varies among these species, this gene could have a greater evolutionary value. Thus, this could assist in informing other scientists which approach is best to conserving the endangered birds in this genus.

This is a part of my science project for research this year.
I am also aware that I do not have enough least concern species yet, but I am searching for another. The problem is, most of the proteins on the NCBI database that are not from the mitochondrion are all partials, and I do not know if partials would be suitable.

Some of the partials from Falco femoralis are http://www.ncbi.nlm.nih.gov/protein/AAS18344.1 and http://www.ncbi.nlm.nih.gov/protein/ABS28828.1.


Basically, in my experiment, I plant to run BLAST and find genomic similarities. Some of them would be nuclear, some mitochondrial. The purpose of using nuclear DNA and proteins are in order to find out if there are some genomic consistencies among the Falco genus. The purpose of using mitochondrial DNA and proteins are to see if there is any phylogenetic relationship between the endangered / least concerned species.

I also hope to apply morphometrics, by seeing if plumage, height, etc. are common within endangered species. This would be done by using known bird databases. Typically, websites like http://www.arkive.org/saker-falcon/falco-cherrug/ are what I plan to use.

With this information, can you tell if partial protein sequences are suitable for running through BLAST?

Also, would using websites like arkive.org be suitable for the experiment?