Question: Create Blast Database From Query Result?
gravatar for Nicholas
8.8 years ago by
Nicholas0 wrote:

Possible Duplicate:
make a custom BLAST library using the output of another blast result


I would like to create a BLAST database using as input a file generated after executing a BLAST query. I first query a fasta file which contains a nucleotide sequence using the blastn command, saving the result in a text file. Next, I try to create a database using the makeblastdb, specifying as input parameter the text file generated after executing the query.

Unfortunately, I get the following error:

BLAST options error: Input format not supported (unknown format). Use -input_type to specify the input type being used.

I try to execute the query in the first step using the -outfmt argument, saving the query results in XML, text ASN.1, binary ASN.1. When I try to create the database specifying in the input_type the 'asn1_bin', 'asn1_txt' and 'xml' respectively, I get the following error:

Error: NCBI C++ Exception: "/am/ncbiapdata/release/blast/src/2.2.25/Linux64-Suse-icc/c++/ICC1010-ReleaseMT64--Linux64-Suse-icc/../src/serial/objistr.cpp", line 838: Error: ncbi::CObjectIStream::SkipFileHeader() - line 3: incompatible type BlastOutput<>Seq-entry ( at Seq-entry)

I would appreciate it if someone can point out what am I missing here.

Ideally, I would like to save the results of the query in a fasta file, but there doesn't seem to be an option of doing this using the -outfmt argument.

Thank you.

fasta makeblastdb blast • 3.4k views
ADD COMMENTlink modified 6.7 years ago by Biostar ♦♦ 20 • written 8.8 years ago by Nicholas0
gravatar for Zach Powers
8.8 years ago by
Zach Powers340
Zach Powers340 wrote:

Take a look at this: Make A Custom Blast Library Using The Output Of Another Blast Result

ADD COMMENTlink modified 13 months ago by RamRS30k • written 8.8 years ago by Zach Powers340
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