Obtaining only the aligned regions in BLAST

Question

[arya]

Hello I have a subject nucleotide sequence which I would like to align to various complete genomes. I am using standalone blastn for the same. Can someone pls tell me how I can retrieve the aligned regions in a separate file. Thanks

[5heikki]

blastn -help

Check the formatting options

[Prasad]

add sseq to output format. -outfmt '6 std sseq'. for more details get the full help as mentioned by @5heikki

[arya]

Thank you! But from the above output format we will get the positions of the aligned regions alone in the genome. Is there any way to obtain the sequence in a separate file?

[5heikki]

From the above you should get 13 column output where the last column displays aligned subject sequence. If you're on Windows, use -outfmt "6 std sseq" instead of -outfmt '6 std sseq'

[cschu181]

Assuming your BLAST output goes into a file called blastout.tsv and you used -outfmt '6 std sseq' , then

cut -f 2,13 blastout.tsv | awk '{printf(">%s\n%s\n", $1, $2); }' > blastout.aligned.fasta

should do the trick (not on Windows, unless you're using Cygwin or something similar).