sorting blast results by sseq coverage

Question

[nheb1977]

my query blastn search returns - 3 sequences tie ( subject sequence) with identical score , e-value and alignment length.

These 3 sequences are of different length. Is there any way to output results so that the hit with highest subject sequence coverage (or in other words, the shortest hit) is displayed first?

[AK]

Hi nheb1977,

Try adding -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore slen" when running BLAST, then sort the results using sort -k1,1 -k12,12nr -k11,11n -k4,4nr -k13,13n.