Is any of the below sentences correct? If yes which one?
The way the data is encoded in the protocol A is different from it is in protocol B.
The way the data is encoded in the protocol A is different from in the protocol B.
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@Mark Hubbard is right.
Still some other forms of the same sentence are also correct.
It appears that there are two difficulties.
English usage regarding the definite article.
(How or when to use the word 'the'.)
These are words like from and than.
English does not typically use 'the' with abstractions, concepts, or names.
So "the Mike" in "drop the Mike" is actually "the mic"--the microphone. Not Mike/Michael.
As mentioned we would refer to death or love or color or life without the definite article. Not the love or the time. There are some exceptions and nuances...but let's not get off track.
[Other (even closely related) languages that have the definite article do use the article in these situations, so it's not surprising when they are overlooked.]
Protocol A is just as much a name as Michael. That means you can say
The man knows about the protocol.
Michael knows about the protocol.
The man knows about Protocol A.
Michael knows about Protocol A.
But you can't add the into those sentences anywhere else.
If we also look at Protocol B we see that it isn't referred to differently than Protocol A.
[By the way, I'm only capitalizing Protocol because sometimes technical terms are capitalized. I would write Entity Data Model, Hypertext Transfer Protocol and Protocol C. I would not tend to write protocol D.]
If we take the away from both protocols in sentence two we are left with
The way the data is encoded in Protocol A is different from in Protocol B.
This is correct English. Or at least it might be--but putting the words from and in together shouldn't be your first choice. It might even be noted as incorrect by a native English speaker. So let's not be content with that as an answer.
Anyhow the short answer to the first question is no. Neither is correct.
Now about those prepositions... you see we can actually use "to", "from" or "than" after "different". The choice depends on the dialect mostly.
That is, in the UK you might say it in a way that's different to how you would say it in the US.
And the American way of saying it might be different from the Canadian way.
Again that might be different than Australians would say it.
For completeness' sake we could look at sentence one. Let's try the same trick of removing 'the'.
The way the data is encoded in Protocol A is different from it is in Protocol B.
(Warning: don't use this sentence. Please.)
You can see that the right hand side of sentence one (It is in Protocol B.) becomes a complete sentence. That means we can't use it after "different from".
The clearest way to compare or contrast things in English is to use a sentence that is as balanced as possible.
I don't intend that as a technical explanation--I just mean it as a clear way of indicating what will best help you to communicate.
In our sentences we are talking about the way, the method, the means.
So let's mention that plainly on both sides of the comparison.
The way the data is encoded in Protocol A is different from the way the data is encoded in Protocol B.
Really we are only saying that one way is different from another way.
We just happen to describe the two ways with more words.
The fact that we see is on either side of the comparison doesn't matter.
Check and see that even though is is in both descriptions, neither of the descriptions is a sentence.
This last version of the sentence is the clearest for two reasons:
It is correct because we are comparing against the left hand side--which does include the information. But it is a lot to leave unsaid.