When I can say that sequence from the BLAST-p result (from NCBI ) is matching or homologues to my query sequence? how many amino acids should be matched ???
If I am planning to identify conserved region in the sequence, do you think 10 sequences are enough for generating multiple sequence alignment ??
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written
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SHAD •
1 answer
See this post:
C: BLAST: Identity % and Similarity %
Blast does not determine "degree" of homology. It is either present or not present.
Phylogenetic tree in most cases characterizes it to some extent.
To generate multiple sequence alignment you can use all sequences you have,
in most case this is the limit - you simply don't have more...
As far as I know there is no upper limit. A lot depends upon alignment-program.
Blast uses local alignment as far as I remember.
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