Blast a sequence with N's
I'm blasting some sequences on nt database, on my local server.
My sequences are short (<100 bp) with this caracteristic:
seq 40N seq
Where seq ~28 bp
my command is the following:
blastn -task blastn-short -evalue 0.1 -qcov_hsp_perc 60 -word_size 7 -dust no -reward 2 -penalty -3 -gapopen 5 -gapextend 2 -query $FASTA -db nt
Blast don't found any match in the databses. But if i run the same command with the "-remote" option, i get back som site of interest. Someone know why this dfference? I revise my databse and it contains all of the founded sequences.
If the seq ~38 bp, and the size of the all sequence is more large than 100bp, blastn local found the same as remote running.
Someone can explian me what's the problem?
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