BLAST sequence alignment

Question

[glady]

What's the basic criteria for a gene and a 16S rRNA to be considered as novel in BLAST ?

[Michael]

It is unclear what you are asking. Please expand your question with an example. sequence alignment does not give rise to a direct interpretation of 'novel', it gives rise to hit vs. no-hit given a E-value cutoff, and the alignment it itself. Everything else is a conclusion based on these results.

[glady]

I have a sequence of a gene ad I do want to check whether is sequence is unique or not. What conclusions should I draw if I get a hit above 80% or else if I get a hit below 50% ?

[Jean-Karim Heriche]

What is it you're trying to achieve ? Is your real question how to determine whether the gene (16S rRNA ?) sequence you have corresponds to a new species ?

[glady]

Say, if I have a gene-A (200bp) and a gene-B (400bp). I want to check whether gene-A is present in gene-B or not. What are the BLAST criteria's which I should consider over here?

[Jean-Karim Heriche]

This is different from what your initial question suggested. It now seems you're looking at deciding whether sequence A can be considered a substring of sequence B. Unless there's a perfect match or a very poor match, there is no clear answer because it depends on assumptions/prior knowledge. For example, you could expect a priori that A is a substring of B and that most mismatches are explainable by sequencing errors.

[GenoMax]

Do a "Dot plot" of the two sequences if all you want to know is if GeneA is has similarities to/is contained in GeneB.

Answer 1

[glady]

I have compared two genes ( subject -> Seq_A(400), query -> Seq_B(200)) through BLASTn and their result where -> % identity - 99%, E_value - 0.0, query cover - 98% and gaps present -7. Does this result justify....that Seq_B is present in Seq_A.

And when you are comparing two genes...is it important that they should be of the same strains ?

[GenoMax]

This still sounds like you are fishing for a "yes" answer. Clearly this is part of some bigger question you are trying to find an answer for but are not providing details about.

You are aware of the concept of orthology? That should answer your second question.