Entering edit mode
9.5 years ago
hilalcihankaya
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0
I need to find a sequence or sequences that should give results (hits) in FASTA but not in BLAST or vice versa. Or, the sequence that cannot be found by both of them..
And I am kinda lost.
What should I look for while searching this sequence(s)?
I recall that it was said somewhere that BLAST is almost always superior to FASTA, except for highly dissimilar sequences. Maybe it would worth to search for an example among them. Still there are many different variations of BLAST, so you should be more specific here.
So you are saying i need to choose discontiguous megablast option, am i right?
But i need to write something to query also (which i have no idea now because blast gives hits with anything i write down)
I mean that you have to select a "distant" query sequence related to your example database. As for "discontiguous megablast" - this depends on what is the question you're asking (e.g. one may want to compare to vanilla BLAST, etc)..
There is not such an option as distant query sequence?
Can you please rephrase your query? As stated, I don't understand it. FASTA is a file format for describing simple sequence data. BLAST is an application that will rapidly search a variety of databases and show the matches for one or more sequence queries.
Although it has fallen somewhat into obscurity the FASTA program is an aligner http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml that introduced the file format that is now commonly associated with sequence storage format. Of course we should make sure that is indeed what the OP is asking about.
Ah, thanks for the clarification. Now the question makes more sense!
Hello hilalcihankaya!
It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/26491285
This is typically not recommended as it runs the risk of annoying people in both communities.
I have a feeling that this is a homework question and that OP has probably been given material that would allow him to answer it. It might be fairly easy to get a false hit with FASTA that wouldn't be reported with Blast assuming default parameters and no SW. FASTA is so legacy at this point that the whole question is rather pointless though..