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Old 09-23-2010, 04:18 PM   #1
z3199001
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Location: Australia

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Default Help with BLASTX command

early learner question here,

I'm trying to run a BLASTX and i'm getting errors returned saying that it can't use DUST filtering.

The help says that by default BLASTX is SEG filtering can anyone tell me how to define this in the command? all the help says is "-F Filter query sequence (DUST with blastn, SEG with others) [String]" is this as simple as -F SEG cause that doesn't seem to work either.

any help would be much appreciated..
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Old 09-23-2010, 11:54 PM   #2
Torst
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Location: The University of Melbourne, AUSTRALIA

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Quote:
Originally Posted by z3199001 View Post
I'm trying to run a BLASTX and i'm getting errors returned saying that it can't use DUST filtering. The help says that by default BLASTX is SEG filtering can anyone tell me how to define this in the command? all the help says is "-F Filter query sequence (DUST with blastn, SEG with others) [String]" is this as simple as -F SEG cause that doesn't seem to work either.
The help is saying that if you turn on filtering with "-F T" (T=true, F=false), then it will use the DUST algorithm to filter the query (when using "-p blastn") and use SEG to filter the query (when not using "-p blastn"). This is because DUST is for DNA sequences, SEG is for protein sequences.

BLASTX searches a a protein databases using a translated nucleotide query. Hence your query is Protein, not DNA. Hence it uses SEG, not DUST. Just supply "-F T" as the option to "blastall".
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Old 09-24-2010, 05:52 AM   #3
kmcarr
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Location: USA, Midwest

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Quote:
Originally Posted by z3199001 View Post
early learner question here,

I'm trying to run a BLASTX and i'm getting errors returned saying that it can't use DUST filtering.

The help says that by default BLASTX is SEG filtering can anyone tell me how to define this in the command? all the help says is "-F Filter query sequence (DUST with blastn, SEG with others) [String]" is this as simple as -F SEG cause that doesn't seem to work either.

any help would be much appreciated..
If you could provide the full command line you tried which produced the error it would help in diagnosing the problem.
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Old 10-11-2010, 08:51 PM   #4
acopeland
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Default blastx seq/dust problems

If you specify a -F option, make sure that the dust binary is in your path. Also, the Korf blast book has some useful discussion and recommendations about blast parameters.
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