Question: Extraction of batch subject sequence from Blast result.
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gravatar for kabir.deb0353
11 months ago by
kabir.deb03530 wrote:

$ "~/ncbi-blast-2.5.0+/bin/makeblastdb" -in sub.fna -dbtype nucl -out sub_DB -parse_seqids

$ "~/ncbi-blast-2.5.0+/bin/tblastn" -query que.fasta -db sub_DB -outfmt 6 -out result_0.01_out -evalue 0.01 -num_threads 24

$ "~/ncbi-blast-2.5.0+/bin/blastdbcmd" -db sub_DB -dbtype nucl -entry_batch entry_range_strand.txt -outfmt "%f" -out Result.fasta

=>entry_range_strand.txt in tab delimited format: ID_011876373 648494-646719 minus ID_011876373 648431-646776 minus ID_011876116 4140-3196 minus ID_011876116 4140-3196 minus ID_011872419 523-564 plus ID_011876146 63749-63793 plus ID_011876398 601642-601692 plus ID_011876397 5713673-5713726 plus ID_011875771 49587-49652 plus

I have followed above method to extract the Blast result sequence. The problem is that result cannot extract the minus strand result properly. However, the result sequence is very good in case of plus strand. Even I have tried by separating both plus and minus strand in the different files but the result doesn't differ. Basically, /blastdbcmd command cannot fetch the sequence range from minus strand, instead, it prints the whole sequence of the corresponding IDs. Hoping for good suggestions and thanks in advance.

ADD COMMENTlink modified 11 months ago by lieven.sterck4.7k • written 11 months ago by kabir.deb03530
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gravatar for lieven.sterck
11 months ago by
lieven.sterck4.7k
VIB, Ghent, Belgium
lieven.sterck4.7k wrote:

the problem might be caused by the fact that the coords for the 'minus' cases are big -> small, while the ones for the plus strand are small->big .

I suggest you switch the coords for the minus strand and try again. Do also double check whether it's the correct strand being returned.

ADD COMMENTlink modified 11 months ago • written 11 months ago by lieven.sterck4.7k
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