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novel proteins

Everything on bioinformatics, the science of information technology as applied to biological research.

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novel proteins

Postby woopwoop » Mon May 09, 2005 3:20 pm

I was just wondering if anyone could give me a hand with an assignment I have ... we have been given the DNA sequence of a novel protein and have to find out as much as possible about it.

so far I have found out the amino acid sequence and entered that into BLASTP to see what kind of other proteins it's most conserved with. (turns out to be halobacteria) but is highly conserved throughout pretty much all bacterium and archaea. From there I've got a phylogenetic tree.

Is it wrong to assume that the function for this protein will be the same as the ones it is most conserved with (have a role in metabolism).

Also I can't get SWISSPRO to generate a hypothetical structure ... so if anyone has any pointers or an alternative ...

so um thanks!
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Postby Niqqie » Fri May 20, 2005 6:23 pm

You did the right thing to pblast it, since it is highly conserved across phyla it means that the function of the protein is important. You are right to assume that the function of the protein will be the same as the others (if the homology is high).

Did you find a protein that gave an exact match? You can also do a nucleotide blast (nblast) to see if it matches to a known gene.
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Postby woopwoop » Wed May 25, 2005 7:32 pm

thanks!!

we shouldn't be able to find our protein's exact match on blast or anywhere since it's brand spanking new.

the homology is extremely high ... going by this it's a thioesterase.

and thanks for the tip about nblast-ing, it makes a great deal of sense to do such things!!
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