The difference blastn output when using subject and db options
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3 months ago
praasu ▴ 40

I have blasted the candidate transposable element to my genome. When I use (db) command 1 (details below) then the output is small and different from the command 2 using subject parameter with same query . If anybody has idea why it is so, Please let me know, thank you very much for your time.

command 1

blastn -db 1621_genome.fa -query output_clusters.fa -num_threads 24 -outfmt "6 qseqid sseqid qstart qend sstart send score length mismatch gaps gapopen nident pident evalue qlen slen qcovs sstrand" >blast_mite_1621_repeat.csv

command 2

blastn -task blastn -query output_clusters.fa  -subject 1621_genome.fa -outfmt "6 qseqid sseqid qstart qend sstart send score length mismatch gaps gapopen nident pident evalue qlen slen qcovs sstrand" >blast_mite_1621_repeat.csv

output_cluster.fa consist of list of transposable element in fasta and 1621_genome.fa contains list of contig in fasta

genome blastn mite annotation tracker • 253 views
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3 months ago
GenoMax 139k

Default task option is megablast for blastn which looks for highly similar sequences compared to blastn which is looking for somewhat similar sequences. Former is used in command 1.

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