~/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.