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10

The paper's description is poor, but they seem to be describing an encoding where each of 20 possible amino acids are associated with a position within a string of 20 bits, e.g. alanine with offset 0, cysteine with offset 1, etc. With that representation, one amino acid residue within a window is encoded by a string of 20 bits, 19 of them being 0 and the ...


3

The term isoform has become a little ambiguous over the years (see http://blogs.cornell.edu/collinslab/2012/05/30/protein-isoform/)... still some things are consistent: In some genetics literature 'isoform' has been used in the place of allele when talking about the allele states at a locus for a gene Typically a gene isoform is equivalent an alternate ...


3

Are multi-chain proteins synthesized as one biological unit? Sometimes yes but mostly not. Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this ...


3

Substituting a single amino acid and checking the effect this has on a protein is a method to determine what this specific amino acid does in the protein. For example, substituting an amino acid that is part of the catalytic core would almost always make the protein non-functional. Alanine scanning is a technique that methodically replaces amino acids in a ...


2

Upstream means towards 5' direction from the reference point (conversely for downstream). Reference point can be a single position such as transcription start site (TSS) or a bigger segment such as a gene. When we say upstream of a gene, it means some region of DNA that is towards 5' direction from the TSS of the reference gene. Downstream of a gene refers ...


1

SEAP, secreted alkaline phosphatase, and vectors engineered to express fusions to this reporter gene may be well-suited to solve your problem.


1

You can always express GFP or your favorite protein in a secretory vector like pSecTag or pSecTag2 from Invitrogen/Life/ThermoFisher/SuperUltraBioMegaMart. There are probably others, but those were the first ones I came across. They contain the mouse Igκ signal sequence for efficient secretion (so the website says, I've never used it). I don't know ...



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